config/dist/raw-data-types.xml

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4888 06 Apr 09 nicklas 1 <?xml version="1.0" encoding="UTF-8" ?>
2959 27 Nov 06 nicklas 2 <!DOCTYPE raw-data-types SYSTEM "raw-data-types.dtd" >
2959 27 Nov 06 nicklas 3 <!--
2959 27 Nov 06 nicklas 4   $Id$
2959 27 Nov 06 nicklas 5
3675 16 Aug 07 jari 6     Copyright (C) 2006 Nicklas Nordborg
3675 16 Aug 07 jari 7     Copyright (C) 2007 Johan Enell, Nicklas Nordborg
2959 27 Nov 06 nicklas 8
2959 27 Nov 06 nicklas 9     This file is part of BASE - BioArray Software Environment.
2959 27 Nov 06 nicklas 10     Available at http://base.thep.lu.se/
2959 27 Nov 06 nicklas 11
2959 27 Nov 06 nicklas 12     BASE is free software; you can redistribute it and/or modify it
2959 27 Nov 06 nicklas 13     under the terms of the GNU General Public License as published by
4474 05 Sep 08 jari 14     the Free Software Foundation; either version 3 of the License, or
2959 27 Nov 06 nicklas 15     (at your option) any later version.
2959 27 Nov 06 nicklas 16
2959 27 Nov 06 nicklas 17     BASE is distributed in the hope that it will be useful, but
2959 27 Nov 06 nicklas 18     WITHOUT ANY WARRANTY; without even the implied warranty of
2959 27 Nov 06 nicklas 19     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
2959 27 Nov 06 nicklas 20     General Public License for more details.
2959 27 Nov 06 nicklas 21
2959 27 Nov 06 nicklas 22     You should have received a copy of the GNU General Public License
4508 11 Sep 08 jari 23     along with BASE. If not, see <http://www.gnu.org/licenses/>.
2959 27 Nov 06 nicklas 24 -->
2959 27 Nov 06 nicklas 25 <raw-data-types>
2959 27 Nov 06 nicklas 26
2959 27 Nov 06 nicklas 27   <raw-data-type
2959 27 Nov 06 nicklas 28     id="genepix"
2959 27 Nov 06 nicklas 29     channels="2"
2959 27 Nov 06 nicklas 30     name="GenePix"
2959 27 Nov 06 nicklas 31     table="RawDataGenePix"
2959 27 Nov 06 nicklas 32     >
2959 27 Nov 06 nicklas 33     <property
2959 27 Nov 06 nicklas 34       name="diameter"
2959 27 Nov 06 nicklas 35       title="Spot diameter"
3501 15 Jun 07 enell 36       description="The diameter of the spot in µm"
2959 27 Nov 06 nicklas 37       column="diameter"
2959 27 Nov 06 nicklas 38       type="float"
4027 30 Nov 07 enell 39       averagemethod="none"
2959 27 Nov 06 nicklas 40     />
2959 27 Nov 06 nicklas 41     <property
2959 27 Nov 06 nicklas 42       name="ch1FgMedian"
2959 27 Nov 06 nicklas 43       title="Channel 1 foreground median"
2959 27 Nov 06 nicklas 44       description="The median of the foreground intensity in channel 1"
2959 27 Nov 06 nicklas 45       column="ch1_fg_median"
2959 27 Nov 06 nicklas 46       type="float"
2959 27 Nov 06 nicklas 47       channel="1"
4027 30 Nov 07 enell 48       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 49     />
2959 27 Nov 06 nicklas 50     <property
2959 27 Nov 06 nicklas 51       name="ch1FgMean"
2959 27 Nov 06 nicklas 52       title="Channel 1 foreground mean"
2959 27 Nov 06 nicklas 53       description="The mean of the foreground intensity in channel 1"
2959 27 Nov 06 nicklas 54       column="ch1_fg_mean"
2959 27 Nov 06 nicklas 55       type="float"
2959 27 Nov 06 nicklas 56       channel="1"
4027 30 Nov 07 enell 57       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 58     />
2959 27 Nov 06 nicklas 59     <property
2959 27 Nov 06 nicklas 60       name="ch1FgSd"
2959 27 Nov 06 nicklas 61       title="Channel 1 foreground standard deviation"
2959 27 Nov 06 nicklas 62       description="The standard deviation of the foreground intensity in channel 1"
2959 27 Nov 06 nicklas 63       column="ch1_fg_sd"
2959 27 Nov 06 nicklas 64       type="float"
2959 27 Nov 06 nicklas 65       channel="1"
4027 30 Nov 07 enell 66       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 67     />
2959 27 Nov 06 nicklas 68     <property
2959 27 Nov 06 nicklas 69       name="ch1BgMedian"
2959 27 Nov 06 nicklas 70       title="Channel 1 background median"
2959 27 Nov 06 nicklas 71       description="The median of the background intensity in channel 1"
2959 27 Nov 06 nicklas 72       column="ch1_bg_median"
2959 27 Nov 06 nicklas 73       type="float"
2959 27 Nov 06 nicklas 74       channel="1"
4027 30 Nov 07 enell 75       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 76     />
2959 27 Nov 06 nicklas 77     <property
2959 27 Nov 06 nicklas 78       name="ch1BgMean"
2959 27 Nov 06 nicklas 79       title="Channel 1 background mean"
2959 27 Nov 06 nicklas 80       description="The mean of the background intensity in channel 1"
2959 27 Nov 06 nicklas 81       column="ch1_bg_mean"
2959 27 Nov 06 nicklas 82       type="float"
2959 27 Nov 06 nicklas 83       channel="1"
4027 30 Nov 07 enell 84       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 85     />
2959 27 Nov 06 nicklas 86     <property
2959 27 Nov 06 nicklas 87       name="ch1BgSd"
2959 27 Nov 06 nicklas 88       title="Channel 1 background standard deviation"
2959 27 Nov 06 nicklas 89       description="The standard deviation of the background intensity in channel 1"
2959 27 Nov 06 nicklas 90       column="ch1_bg_sd"
2959 27 Nov 06 nicklas 91       type="float"
2959 27 Nov 06 nicklas 92       channel="1"
4027 30 Nov 07 enell 93       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 94     />
2959 27 Nov 06 nicklas 95     <property
2959 27 Nov 06 nicklas 96       name="ch1PercSd1"
3501 15 Jun 07 enell 97       title="% pixels &gt; 1 standard deviation above backgound"
3501 15 Jun 07 enell 98       description="Percentage of pixels more than 1 standard deviation 
3501 15 Jun 07 enell 99         above the background intensity in channel 1"
2959 27 Nov 06 nicklas 100       column="ch1_perc_sd1"
2959 27 Nov 06 nicklas 101       type="int"
2959 27 Nov 06 nicklas 102       channel="1"
4027 30 Nov 07 enell 103       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 104     />
2959 27 Nov 06 nicklas 105     <property
2959 27 Nov 06 nicklas 106       name="ch1PercSd2"
3501 15 Jun 07 enell 107       title="% pixels &gt; 2 standard deviations above backgound"
3501 15 Jun 07 enell 108       description="Percentage of pixels more than 2 standard deviations 
3501 15 Jun 07 enell 109         above the background intensity in channel 1"
2959 27 Nov 06 nicklas 110       column="ch1_perc_sd2"
2959 27 Nov 06 nicklas 111       type="int"
2959 27 Nov 06 nicklas 112       channel="1"
4027 30 Nov 07 enell 113       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 114     />
2959 27 Nov 06 nicklas 115     <property
2959 27 Nov 06 nicklas 116       name="ch1PercSat"
2959 27 Nov 06 nicklas 117       title="Percent saturated pixels"
2959 27 Nov 06 nicklas 118       description="Percentage of saturated pixels in channel 1"
2959 27 Nov 06 nicklas 119       column="ch1_perc_sat"
2959 27 Nov 06 nicklas 120       type="int"
2959 27 Nov 06 nicklas 121       channel="1"
4027 30 Nov 07 enell 122       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 123     />
2959 27 Nov 06 nicklas 124
2959 27 Nov 06 nicklas 125     <property
2959 27 Nov 06 nicklas 126       name="ch2FgMedian"
2959 27 Nov 06 nicklas 127       title="Channel 2 foreground median"
2959 27 Nov 06 nicklas 128       description="The median of the foreground intensity in channel 2"
2959 27 Nov 06 nicklas 129       column="ch2_fg_median"
2959 27 Nov 06 nicklas 130       type="float"
2959 27 Nov 06 nicklas 131       channel="2"
4027 30 Nov 07 enell 132       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 133     />
2959 27 Nov 06 nicklas 134     <property
2959 27 Nov 06 nicklas 135       name="ch2FgMean"
2959 27 Nov 06 nicklas 136       title="Channel 2 foreground mean"
2959 27 Nov 06 nicklas 137       description="The mean of the foreground intensity in channel 2"
2959 27 Nov 06 nicklas 138       column="ch2_fg_mean"
2959 27 Nov 06 nicklas 139       type="float"
2959 27 Nov 06 nicklas 140       channel="2"
4027 30 Nov 07 enell 141       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 142     />
2959 27 Nov 06 nicklas 143     <property
2959 27 Nov 06 nicklas 144       name="ch2FgSd"
2959 27 Nov 06 nicklas 145       title="Channel 2 foreground standard deviation"
2959 27 Nov 06 nicklas 146       description="The standard deviation of the foreground intensity in channel 2"
2959 27 Nov 06 nicklas 147       column="ch2_fg_sd"
2959 27 Nov 06 nicklas 148       type="float"
2959 27 Nov 06 nicklas 149       channel="2"
4027 30 Nov 07 enell 150       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 151     />
2959 27 Nov 06 nicklas 152     <property
2959 27 Nov 06 nicklas 153       name="ch2BgMedian"
2959 27 Nov 06 nicklas 154       title="Channel 2 background median"
2959 27 Nov 06 nicklas 155       description="The median of the background intensity in channel 2"
2959 27 Nov 06 nicklas 156       column="ch2_bg_median"
2959 27 Nov 06 nicklas 157       type="float"
2959 27 Nov 06 nicklas 158       channel="2"
4027 30 Nov 07 enell 159       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 160     />
2959 27 Nov 06 nicklas 161     <property
2959 27 Nov 06 nicklas 162       name="ch2BgMean"
2959 27 Nov 06 nicklas 163       title="Channel 2 background mean"
2959 27 Nov 06 nicklas 164       description="The mean of the background intensity in channel 2"
2959 27 Nov 06 nicklas 165       column="ch2_bg_mean"
2959 27 Nov 06 nicklas 166       type="float"
2959 27 Nov 06 nicklas 167       channel="2"
4027 30 Nov 07 enell 168       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 169     />
2959 27 Nov 06 nicklas 170     <property
2959 27 Nov 06 nicklas 171       name="ch2BgSd"
2959 27 Nov 06 nicklas 172       title="Channel 2 background standard deviation"
2959 27 Nov 06 nicklas 173       description="The standard deviation of the background intensity in channel 2"
2959 27 Nov 06 nicklas 174       column="ch2_bg_sd"
2959 27 Nov 06 nicklas 175       type="float"
2959 27 Nov 06 nicklas 176       channel="2"
4027 30 Nov 07 enell 177       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 178     />
2959 27 Nov 06 nicklas 179     <property
2959 27 Nov 06 nicklas 180       name="ch2PercSd1"
3501 15 Jun 07 enell 181       title="% pixels &gt; 1 standard deviation above backgound"
3501 15 Jun 07 enell 182       description="Percentage of pixels more than 1 standard deviation 
3501 15 Jun 07 enell 183         above the background intensity in channel 2"
2959 27 Nov 06 nicklas 184       column="ch2_perc_sd1"
2959 27 Nov 06 nicklas 185       type="int"
2959 27 Nov 06 nicklas 186       channel="2"
4027 30 Nov 07 enell 187       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 188     />
2959 27 Nov 06 nicklas 189     <property
2959 27 Nov 06 nicklas 190       name="ch2PercSd2"
3501 15 Jun 07 enell 191       title="% pixels &gt; 2 standard deviations above backgound"
3501 15 Jun 07 enell 192       description="Percentage of pixels more than 2 standard deviations 
3501 15 Jun 07 enell 193         above the background intensity in channel 2"
2959 27 Nov 06 nicklas 194       column="ch2_perc_sd2"
2959 27 Nov 06 nicklas 195       type="int"
2959 27 Nov 06 nicklas 196       channel="2"
4027 30 Nov 07 enell 197       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 198     />
2959 27 Nov 06 nicklas 199     <property
2959 27 Nov 06 nicklas 200       name="ch2PercSat"
2959 27 Nov 06 nicklas 201       title="Percent saturated pixels"
2959 27 Nov 06 nicklas 202       description="Percentage of saturated pixels in channel 2"
2959 27 Nov 06 nicklas 203       column="ch2_perc_sat"
2959 27 Nov 06 nicklas 204       type="int"
2959 27 Nov 06 nicklas 205       channel="2"
4027 30 Nov 07 enell 206       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 207     />
2959 27 Nov 06 nicklas 208
2959 27 Nov 06 nicklas 209     <property
2959 27 Nov 06 nicklas 210       name="ratiosSd"
2959 27 Nov 06 nicklas 211       title="Standard deviation of ratios"
3501 15 Jun 07 enell 212       description="The geometric standard deviation of the pixel intensity ratios."
2959 27 Nov 06 nicklas 213       column="ratios_sd"
2959 27 Nov 06 nicklas 214       type="float"
4027 30 Nov 07 enell 215       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 216     />
2959 27 Nov 06 nicklas 217     <property
2959 27 Nov 06 nicklas 218       name="rgnRatio"
3501 15 Jun 07 enell 219       title="Regression ratio"
3501 15 Jun 07 enell 220       description="The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature."
2959 27 Nov 06 nicklas 221       column="rgn_ratio"
2959 27 Nov 06 nicklas 222       type="float"
4027 30 Nov 07 enell 223       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 224     />
2959 27 Nov 06 nicklas 225     <property
2959 27 Nov 06 nicklas 226       name="rgnR2"
2959 27 Nov 06 nicklas 227       title="Rgn R2"
3501 15 Jun 07 enell 228       description="The coefficient of determination for the current regression value."
2959 27 Nov 06 nicklas 229       column="rgn_r2"
2959 27 Nov 06 nicklas 230       type="float"
4027 30 Nov 07 enell 231       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 232     />
2959 27 Nov 06 nicklas 233
2959 27 Nov 06 nicklas 234     <property
2959 27 Nov 06 nicklas 235       name="fgPixels"
2959 27 Nov 06 nicklas 236       title="Foreground pixels"
2959 27 Nov 06 nicklas 237       description="Number of foreground pixels"
2959 27 Nov 06 nicklas 238       column="fg_pixels"
2959 27 Nov 06 nicklas 239       type="int"
4027 30 Nov 07 enell 240       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 241     />
2959 27 Nov 06 nicklas 242     <property
2959 27 Nov 06 nicklas 243       name="bgPixels"
2959 27 Nov 06 nicklas 244       title="Background pixels"
2959 27 Nov 06 nicklas 245       description="Number of background pixels"
2959 27 Nov 06 nicklas 246       column="bg_pixels"
2959 27 Nov 06 nicklas 247       type="int"
4027 30 Nov 07 enell 248       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 249     />
2959 27 Nov 06 nicklas 250     <property
2959 27 Nov 06 nicklas 251       name="flags"
2959 27 Nov 06 nicklas 252       title="Flags"
2959 27 Nov 06 nicklas 253       description="Flags"
2959 27 Nov 06 nicklas 254       column="flags"
2959 27 Nov 06 nicklas 255       type="int"
3623 02 Aug 07 enell 256       averagemethod="none"
2959 27 Nov 06 nicklas 257     />
2959 27 Nov 06 nicklas 258     <property
2959 27 Nov 06 nicklas 259       name="mValue"
2959 27 Nov 06 nicklas 260       title="M value"
2959 27 Nov 06 nicklas 261       description="M value"
2959 27 Nov 06 nicklas 262       column="m_value"
2959 27 Nov 06 nicklas 263       type="float"
4027 30 Nov 07 enell 264       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 265     />
2959 27 Nov 06 nicklas 266     <property
2959 27 Nov 06 nicklas 267       name="CV"
2959 27 Nov 06 nicklas 268       title="CV"
2959 27 Nov 06 nicklas 269       description="CV"
2959 27 Nov 06 nicklas 270       column="cv"
2959 27 Nov 06 nicklas 271       type="float"
4027 30 Nov 07 enell 272       averagemethod="none"
2959 27 Nov 06 nicklas 273     />
2959 27 Nov 06 nicklas 274     <intensity-formula
2959 27 Nov 06 nicklas 275       name="mean"
2959 27 Nov 06 nicklas 276       title="Mean FG - Mean BG"
2959 27 Nov 06 nicklas 277       description="Subtract mean background from mean foreground"
2959 27 Nov 06 nicklas 278       >
2959 27 Nov 06 nicklas 279       <formula 
2959 27 Nov 06 nicklas 280         channel="1"
2959 27 Nov 06 nicklas 281         expression="raw('ch1FgMean') - raw('ch1BgMean')"
2959 27 Nov 06 nicklas 282       />
2959 27 Nov 06 nicklas 283       <formula 
2959 27 Nov 06 nicklas 284         channel="2"
2959 27 Nov 06 nicklas 285         expression="raw('ch2FgMean') - raw('ch2BgMean')"
2959 27 Nov 06 nicklas 286       />
2959 27 Nov 06 nicklas 287     </intensity-formula>
2959 27 Nov 06 nicklas 288     <intensity-formula
2959 27 Nov 06 nicklas 289       name="median"
2959 27 Nov 06 nicklas 290       title="Median FG - Median BG"
2959 27 Nov 06 nicklas 291       description="Subtract meadian background from median foreground"
2959 27 Nov 06 nicklas 292       >
2959 27 Nov 06 nicklas 293       <formula 
2959 27 Nov 06 nicklas 294         channel="1"
2959 27 Nov 06 nicklas 295         expression="raw('ch1FgMedian') - raw('ch1BgMedian')"
2959 27 Nov 06 nicklas 296       />
2959 27 Nov 06 nicklas 297       <formula 
2959 27 Nov 06 nicklas 298         channel="2"
2959 27 Nov 06 nicklas 299         expression="raw('ch2FgMedian') - raw('ch2BgMedian')"
2959 27 Nov 06 nicklas 300       />
2959 27 Nov 06 nicklas 301     </intensity-formula>
2959 27 Nov 06 nicklas 302     <intensity-formula
2959 27 Nov 06 nicklas 303       name="medianmean"
2959 27 Nov 06 nicklas 304       title="Median FG - Mean BG"
2959 27 Nov 06 nicklas 305       description="Subtract mean background from median foreground"
2959 27 Nov 06 nicklas 306       >
2959 27 Nov 06 nicklas 307       <formula 
2959 27 Nov 06 nicklas 308         channel="1"
2959 27 Nov 06 nicklas 309         expression="raw('ch1FgMedian') - raw('ch1BgMean')"
2959 27 Nov 06 nicklas 310       />
2959 27 Nov 06 nicklas 311       <formula 
2959 27 Nov 06 nicklas 312         channel="2"
2959 27 Nov 06 nicklas 313         expression="raw('ch2FgMedian') - raw('ch2BgMean')"
2959 27 Nov 06 nicklas 314       />
2959 27 Nov 06 nicklas 315     </intensity-formula>
2959 27 Nov 06 nicklas 316     <intensity-formula
2959 27 Nov 06 nicklas 317       name="meanmedian"
2959 27 Nov 06 nicklas 318       title="Mean FG - Median BG"
2959 27 Nov 06 nicklas 319       description="Subtract median background from mean foreground"
2959 27 Nov 06 nicklas 320       >
2959 27 Nov 06 nicklas 321       <formula 
2959 27 Nov 06 nicklas 322         channel="1"
2959 27 Nov 06 nicklas 323         expression="raw('ch1FgMean') - raw('ch1BgMedian')"
2959 27 Nov 06 nicklas 324       />
2959 27 Nov 06 nicklas 325       <formula 
2959 27 Nov 06 nicklas 326         channel="2"
2959 27 Nov 06 nicklas 327         expression="raw('ch2FgMean') - raw('ch2BgMedian')"
2959 27 Nov 06 nicklas 328       />
2959 27 Nov 06 nicklas 329     </intensity-formula>
2959 27 Nov 06 nicklas 330     <intensity-formula
2959 27 Nov 06 nicklas 331       name="meanfg"
2959 27 Nov 06 nicklas 332       title="Mean FG"
2959 27 Nov 06 nicklas 333       description="Mean foreground"
2959 27 Nov 06 nicklas 334       >
2959 27 Nov 06 nicklas 335       <formula 
2959 27 Nov 06 nicklas 336         channel="1"
2959 27 Nov 06 nicklas 337         expression="raw('ch1FgMean')"
2959 27 Nov 06 nicklas 338       />
2959 27 Nov 06 nicklas 339       <formula 
2959 27 Nov 06 nicklas 340         channel="2"
2959 27 Nov 06 nicklas 341         expression="raw('ch2FgMean')"
2959 27 Nov 06 nicklas 342       />
2959 27 Nov 06 nicklas 343     </intensity-formula>
2959 27 Nov 06 nicklas 344     <intensity-formula
2959 27 Nov 06 nicklas 345       name="medianfg"
2959 27 Nov 06 nicklas 346       title="Median FG"
2959 27 Nov 06 nicklas 347       description="Median foreground"
2959 27 Nov 06 nicklas 348       >
2959 27 Nov 06 nicklas 349       <formula 
2959 27 Nov 06 nicklas 350         channel="1"
2959 27 Nov 06 nicklas 351         expression="raw('ch1FgMedian')"
2959 27 Nov 06 nicklas 352       />
2959 27 Nov 06 nicklas 353       <formula 
2959 27 Nov 06 nicklas 354         channel="2"
2959 27 Nov 06 nicklas 355         expression="raw('ch2FgMedian')"
2959 27 Nov 06 nicklas 356       />
2959 27 Nov 06 nicklas 357     </intensity-formula>
2959 27 Nov 06 nicklas 358     <intensity-formula
2959 27 Nov 06 nicklas 359       name="medianfgmeanmedianbg"
2959 27 Nov 06 nicklas 360       title="Median FG - Mean(Median BG)"
2959 27 Nov 06 nicklas 361       description="Subtract mean of median backgrounds from median foreground"
2959 27 Nov 06 nicklas 362       >
2959 27 Nov 06 nicklas 363       <formula 
2959 27 Nov 06 nicklas 364         channel="1"
2959 27 Nov 06 nicklas 365         expression="raw('ch1FgMedian') - mean('ch1BgMedian')"
2959 27 Nov 06 nicklas 366       />
2959 27 Nov 06 nicklas 367       <formula 
2959 27 Nov 06 nicklas 368         channel="2"
2959 27 Nov 06 nicklas 369         expression="raw('ch2FgMedian') - mean('ch2BgMedian')"
2959 27 Nov 06 nicklas 370       />
2959 27 Nov 06 nicklas 371     </intensity-formula>
2959 27 Nov 06 nicklas 372     <intensity-formula
2959 27 Nov 06 nicklas 373       name="meanfgmeanmeanbg"
2959 27 Nov 06 nicklas 374       title="Mean FG - Mean(Mean BG)"
2959 27 Nov 06 nicklas 375       description="Subtract mean of mean backgrounds from mean foreground"
2959 27 Nov 06 nicklas 376       >
2959 27 Nov 06 nicklas 377       <formula 
2959 27 Nov 06 nicklas 378         channel="1"
2959 27 Nov 06 nicklas 379         expression="raw('ch1FgMean') - mean('ch1BgMean')"
2959 27 Nov 06 nicklas 380       />
2959 27 Nov 06 nicklas 381       <formula 
2959 27 Nov 06 nicklas 382         channel="2"
2959 27 Nov 06 nicklas 383         expression="raw('ch2FgMean') - mean('ch2BgMean')"
2959 27 Nov 06 nicklas 384       />
2959 27 Nov 06 nicklas 385     </intensity-formula>
2959 27 Nov 06 nicklas 386     <intensity-formula
2959 27 Nov 06 nicklas 387       name="medianfgmeanmeanbg"
2959 27 Nov 06 nicklas 388       title="Median FG - Mean(Mean BG)"
2959 27 Nov 06 nicklas 389       description="Subtract mean of mean backgrounds from median foreground"
2959 27 Nov 06 nicklas 390       >
2959 27 Nov 06 nicklas 391       <formula 
2959 27 Nov 06 nicklas 392         channel="1"
2959 27 Nov 06 nicklas 393         expression="raw('ch1FgMedian') - mean('ch1BgMean')"
2959 27 Nov 06 nicklas 394       />
2959 27 Nov 06 nicklas 395       <formula 
2959 27 Nov 06 nicklas 396         channel="2"
2959 27 Nov 06 nicklas 397         expression="raw('ch2FgMedian') - mean('ch2BgMean')"
2959 27 Nov 06 nicklas 398       />
2959 27 Nov 06 nicklas 399     </intensity-formula>
2959 27 Nov 06 nicklas 400     <intensity-formula
2959 27 Nov 06 nicklas 401       name="meanfgmeanmedianbg"
2959 27 Nov 06 nicklas 402       title="Mean FG - Mean(Median BG)"
2959 27 Nov 06 nicklas 403       description="Subtract mean of median backgrounds from mean foreground"
2959 27 Nov 06 nicklas 404       >
2959 27 Nov 06 nicklas 405       <formula 
2959 27 Nov 06 nicklas 406         channel="1"
2959 27 Nov 06 nicklas 407         expression="raw('ch1FgMean') - mean('ch1BgMedian')"
2959 27 Nov 06 nicklas 408       />
2959 27 Nov 06 nicklas 409       <formula 
2959 27 Nov 06 nicklas 410         channel="2"
2959 27 Nov 06 nicklas 411         expression="raw('ch2FgMean') - mean('ch2BgMedian')"
2959 27 Nov 06 nicklas 412       />
2959 27 Nov 06 nicklas 413     </intensity-formula>
2959 27 Nov 06 nicklas 414   </raw-data-type>
2959 27 Nov 06 nicklas 415   
2959 27 Nov 06 nicklas 416   <raw-data-type
2959 27 Nov 06 nicklas 417     id="bzscan"
2959 27 Nov 06 nicklas 418     channels="1"
2959 27 Nov 06 nicklas 419     name="BZScan"
2959 27 Nov 06 nicklas 420     table="RawDataBZScan"
2959 27 Nov 06 nicklas 421     >
2959 27 Nov 06 nicklas 422     <property
2959 27 Nov 06 nicklas 423       name="QImageConst"
2959 27 Nov 06 nicklas 424       title="Q(image,const)"
2959 27 Nov 06 nicklas 425       description="Spot intensity based on user-provided diameter and measured data."
2959 27 Nov 06 nicklas 426       column="q_image_const"
2959 27 Nov 06 nicklas 427       type="float"
2959 27 Nov 06 nicklas 428     />
2959 27 Nov 06 nicklas 429     <property
2959 27 Nov 06 nicklas 430       name="QImageVar"
2959 27 Nov 06 nicklas 431       title="Q(image,var)"
2959 27 Nov 06 nicklas 432       description="Spot intensity based on computed diameter and measured data."
2959 27 Nov 06 nicklas 433       column="q_image_var"
2959 27 Nov 06 nicklas 434       type="float"
2959 27 Nov 06 nicklas 435     />
2959 27 Nov 06 nicklas 436     <property
2959 27 Nov 06 nicklas 437       name="QFitConst"
2959 27 Nov 06 nicklas 438       title="Q(fit,const)"
2959 27 Nov 06 nicklas 439       description="Spot intensity based on user-provided diameter and theoretical fit to the data."
2959 27 Nov 06 nicklas 440       column="q_fit_const"
2959 27 Nov 06 nicklas 441       type="float"
2959 27 Nov 06 nicklas 442     />
2959 27 Nov 06 nicklas 443     <property
2959 27 Nov 06 nicklas 444       name="QFitVar"
2959 27 Nov 06 nicklas 445       title="Q(fit,var)"
2959 27 Nov 06 nicklas 446       description="Spot intensity based on computed diameter and and theoretical fit to the data."
2959 27 Nov 06 nicklas 447       column="q_fit_var"
2959 27 Nov 06 nicklas 448       type="float"
2959 27 Nov 06 nicklas 449     />
2959 27 Nov 06 nicklas 450     <property
2959 27 Nov 06 nicklas 451       name="FitCorrection"
2959 27 Nov 06 nicklas 452       title="Fit correction"
2959 27 Nov 06 nicklas 453       description="Background level by unit surface."
2959 27 Nov 06 nicklas 454       column="fit_correction"
2959 27 Nov 06 nicklas 455       type="float"
2959 27 Nov 06 nicklas 456     />
2959 27 Nov 06 nicklas 457     <property
2959 27 Nov 06 nicklas 458       name="QM"
2959 27 Nov 06 nicklas 459       title="Quality metric"
2959 27 Nov 06 nicklas 460       description="Quality metric: distance between measured data and theoretical fit."
2959 27 Nov 06 nicklas 461       column="quality_metric"
2959 27 Nov 06 nicklas 462       type="float"
2959 27 Nov 06 nicklas 463     />
2959 27 Nov 06 nicklas 464     <property
2959 27 Nov 06 nicklas 465       name="SpotQuality"
2959 27 Nov 06 nicklas 466       title="Spot quality"
2959 27 Nov 06 nicklas 467       description="Present/Absent (automatic guess)."
2959 27 Nov 06 nicklas 468       column="spot_quality"
2959 27 Nov 06 nicklas 469       type="boolean"
2959 27 Nov 06 nicklas 470     />
2959 27 Nov 06 nicklas 471     <property
2959 27 Nov 06 nicklas 472       name="OvershiningCorrection"
2959 27 Nov 06 nicklas 473       title="Overshining correction"
2959 27 Nov 06 nicklas 474       description="Correction for overshining by unit radius."
2959 27 Nov 06 nicklas 475       column="overshining"
2959 27 Nov 06 nicklas 476       type="float"
2959 27 Nov 06 nicklas 477     />
2959 27 Nov 06 nicklas 478     <intensity-formula
2959 27 Nov 06 nicklas 479       name="QImageConst"
2959 27 Nov 06 nicklas 480       title="Q(image,const)"
2959 27 Nov 06 nicklas 481       description="Spot intensity based on user-provided diameter and measured data"
2959 27 Nov 06 nicklas 482       >
2959 27 Nov 06 nicklas 483       <formula 
2959 27 Nov 06 nicklas 484         channel="1"
2959 27 Nov 06 nicklas 485         expression="raw('QImageConst')"
2959 27 Nov 06 nicklas 486       />
2959 27 Nov 06 nicklas 487     </intensity-formula>
2959 27 Nov 06 nicklas 488     <intensity-formula
2959 27 Nov 06 nicklas 489       name="QImageVar"
2959 27 Nov 06 nicklas 490       title="Q(image,var)"
2959 27 Nov 06 nicklas 491       description="Spot intensity based on computed diameter and measured data"
2959 27 Nov 06 nicklas 492       >
2959 27 Nov 06 nicklas 493       <formula 
2959 27 Nov 06 nicklas 494         channel="1"
2959 27 Nov 06 nicklas 495         expression="raw('QImageVar')"
2959 27 Nov 06 nicklas 496       />
2959 27 Nov 06 nicklas 497     </intensity-formula>
2959 27 Nov 06 nicklas 498     <intensity-formula
2959 27 Nov 06 nicklas 499       name="QFitConst"
2959 27 Nov 06 nicklas 500       title="Q(fit,const)"
2959 27 Nov 06 nicklas 501       description="Spot intensity based on user-provided diameter and theoretical fit to the data"
2959 27 Nov 06 nicklas 502       >
2959 27 Nov 06 nicklas 503       <formula 
2959 27 Nov 06 nicklas 504         channel="1"
2959 27 Nov 06 nicklas 505         expression="raw('QFitConst')"
2959 27 Nov 06 nicklas 506       />
2959 27 Nov 06 nicklas 507     </intensity-formula>
2959 27 Nov 06 nicklas 508     <intensity-formula
2959 27 Nov 06 nicklas 509       name="QFitVar"
2959 27 Nov 06 nicklas 510       title="Q(fit,var)"
2959 27 Nov 06 nicklas 511       description="Spot intensity based on computed diameter and and theoretical fit to the data"
2959 27 Nov 06 nicklas 512       >
2959 27 Nov 06 nicklas 513       <formula 
2959 27 Nov 06 nicklas 514         channel="1"
2959 27 Nov 06 nicklas 515         expression="raw('QFitVar')"
2959 27 Nov 06 nicklas 516       />
2959 27 Nov 06 nicklas 517     </intensity-formula>
2959 27 Nov 06 nicklas 518   </raw-data-type>
2959 27 Nov 06 nicklas 519   
2959 27 Nov 06 nicklas 520   <raw-data-type
2959 27 Nov 06 nicklas 521     id="aida"
2959 27 Nov 06 nicklas 522     channels="2"
2959 27 Nov 06 nicklas 523     name="AIDA"
2959 27 Nov 06 nicklas 524     table="RawDataAida"
2959 27 Nov 06 nicklas 525     >
2959 27 Nov 06 nicklas 526     <property
2959 27 Nov 06 nicklas 527       name="area"
2959 27 Nov 06 nicklas 528       title="Area"
2959 27 Nov 06 nicklas 529       description="Spot area in pixels."
2959 27 Nov 06 nicklas 530       column="area"
2959 27 Nov 06 nicklas 531       type="float"
4027 30 Nov 07 enell 532       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 533     />
2959 27 Nov 06 nicklas 534     <property
2959 27 Nov 06 nicklas 535       name="ch1Integral"
2959 27 Nov 06 nicklas 536       title="Channel 1 integral"
2959 27 Nov 06 nicklas 537       description="Integrated raw intensity of spot channel 1."
2959 27 Nov 06 nicklas 538       column="ch1_integral"
2959 27 Nov 06 nicklas 539       type="float"
2959 27 Nov 06 nicklas 540       channel="1"
4027 30 Nov 07 enell 541       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 542     />
2959 27 Nov 06 nicklas 543     <property
2959 27 Nov 06 nicklas 544       name="ch1Mean"
2959 27 Nov 06 nicklas 545       title="Channel 1 mean"
2959 27 Nov 06 nicklas 546       description="Mean (Integral/Area) channel 1."
2959 27 Nov 06 nicklas 547       column="ch1_mean"
2959 27 Nov 06 nicklas 548       type="float"
2959 27 Nov 06 nicklas 549       channel="1"
4027 30 Nov 07 enell 550       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 551     />
2959 27 Nov 06 nicklas 552     <property
2959 27 Nov 06 nicklas 553       name="ch1Median"
2959 27 Nov 06 nicklas 554       title="Channel 1 median"
2959 27 Nov 06 nicklas 555       description="Median of the raw pixel intensity of spot channel 1."
2959 27 Nov 06 nicklas 556       column="ch1_median"
2959 27 Nov 06 nicklas 557       type="float"
2959 27 Nov 06 nicklas 558       channel="1"
4027 30 Nov 07 enell 559       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 560     />
2959 27 Nov 06 nicklas 561     <property
2959 27 Nov 06 nicklas 562       name="ch1Bkg"
2959 27 Nov 06 nicklas 563       title="Channel 1 background"
2959 27 Nov 06 nicklas 564       description="Standard deviation of background channel 1."
2959 27 Nov 06 nicklas 565       column="ch1_bkg"
2959 27 Nov 06 nicklas 566       type="float"
2959 27 Nov 06 nicklas 567       channel="1"
4027 30 Nov 07 enell 568       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 569     />
2959 27 Nov 06 nicklas 570     <property
2959 27 Nov 06 nicklas 571       name="ch1Sat"
2959 27 Nov 06 nicklas 572       title="Channel 1 saturated"
2959 27 Nov 06 nicklas 573       description="Measure of saturation pixels channel 1."
2959 27 Nov 06 nicklas 574       column="ch1_sat"
2959 27 Nov 06 nicklas 575       type="float"
2959 27 Nov 06 nicklas 576       channel="1"
4027 30 Nov 07 enell 577       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 578     />
2959 27 Nov 06 nicklas 579     <property
2959 27 Nov 06 nicklas 580       name="ch1Hom"
2959 27 Nov 06 nicklas 581       title="Channel 1 homogenity"
2959 27 Nov 06 nicklas 582       description="Percentage of dot deviation from homogenous intensity distribution channel 1."
2959 27 Nov 06 nicklas 583       column="ch1_hom"
2959 27 Nov 06 nicklas 584       type="float"
2959 27 Nov 06 nicklas 585       channel="1"
4027 30 Nov 07 enell 586       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 587     />
2959 27 Nov 06 nicklas 588     <property
2959 27 Nov 06 nicklas 589       name="ch1Quality"
2959 27 Nov 06 nicklas 590       title="Channel 1 quality"
2959 27 Nov 06 nicklas 591       description="Quality flag channel 1."
2959 27 Nov 06 nicklas 592       column="ch1_quality"
2959 27 Nov 06 nicklas 593       type="boolean"
2959 27 Nov 06 nicklas 594       channel="1"
4027 30 Nov 07 enell 595       averagemethod="none"
2959 27 Nov 06 nicklas 596     />
2959 27 Nov 06 nicklas 597     <property
2959 27 Nov 06 nicklas 598       name="ch2Integral"
2959 27 Nov 06 nicklas 599       title="Channel 2 integral"
2959 27 Nov 06 nicklas 600       description="Integrated raw intensity of spot channel 2."
2959 27 Nov 06 nicklas 601       column="ch2_integral"
2959 27 Nov 06 nicklas 602       type="float"
2959 27 Nov 06 nicklas 603       channel="2"
4027 30 Nov 07 enell 604       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 605     />
2959 27 Nov 06 nicklas 606     <property
2959 27 Nov 06 nicklas 607       name="ch2Mean"
2959 27 Nov 06 nicklas 608       title="Channel 2 mean"
2959 27 Nov 06 nicklas 609       description="Mean (Integral/Area) channel 2."
2959 27 Nov 06 nicklas 610       column="ch2_mean"
2959 27 Nov 06 nicklas 611       type="float"
2959 27 Nov 06 nicklas 612       channel="2"
4027 30 Nov 07 enell 613       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 614     />
2959 27 Nov 06 nicklas 615     <property
2959 27 Nov 06 nicklas 616       name="ch2Median"
2959 27 Nov 06 nicklas 617       title="Channel 2 median"
2959 27 Nov 06 nicklas 618       description="Median of the raw pixel intensity of spot channel 2."
2959 27 Nov 06 nicklas 619       column="ch2_median"
2959 27 Nov 06 nicklas 620       type="float"
2959 27 Nov 06 nicklas 621       channel="2"
4027 30 Nov 07 enell 622       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 623     />
2959 27 Nov 06 nicklas 624     <property
2959 27 Nov 06 nicklas 625       name="ch2Bkg"
2959 27 Nov 06 nicklas 626       title="Channel 2 background"
2959 27 Nov 06 nicklas 627       description="Standard deviation of background channel 2."
2959 27 Nov 06 nicklas 628       column="ch2_bkg"
2959 27 Nov 06 nicklas 629       type="float"
2959 27 Nov 06 nicklas 630       channel="2"
4027 30 Nov 07 enell 631       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 632     />
2959 27 Nov 06 nicklas 633     <property
2959 27 Nov 06 nicklas 634       name="ch2Sat"
2959 27 Nov 06 nicklas 635       title="Channel 2 saturated"
2959 27 Nov 06 nicklas 636       description="Measure of saturation pixels channel 2."
2959 27 Nov 06 nicklas 637       column="ch2_sat"
2959 27 Nov 06 nicklas 638       type="float"
2959 27 Nov 06 nicklas 639       channel="2"
4027 30 Nov 07 enell 640       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 641     />
2959 27 Nov 06 nicklas 642     <property
2959 27 Nov 06 nicklas 643       name="ch2Hom"
2959 27 Nov 06 nicklas 644       title="Channel 2 homogenity"
2959 27 Nov 06 nicklas 645       description="Percentage of dot deviation from homogenous intensity distribution channel 2."
2959 27 Nov 06 nicklas 646       column="ch2_hom"
2959 27 Nov 06 nicklas 647       type="float"
2959 27 Nov 06 nicklas 648       channel="2"
4027 30 Nov 07 enell 649       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 650     />
2959 27 Nov 06 nicklas 651     <property
2959 27 Nov 06 nicklas 652       name="ch2Quality"
2959 27 Nov 06 nicklas 653       title="Channel 2 quality"
2959 27 Nov 06 nicklas 654       description="Quality flag channel 2."
2959 27 Nov 06 nicklas 655       column="ch2_quality"
2959 27 Nov 06 nicklas 656       type="boolean"
2959 27 Nov 06 nicklas 657       channel="2"
4027 30 Nov 07 enell 658       averagemethod="none"
2959 27 Nov 06 nicklas 659     />
2959 27 Nov 06 nicklas 660     <intensity-formula
2959 27 Nov 06 nicklas 661       name="mean"
2959 27 Nov 06 nicklas 662       title="Mean"
2959 27 Nov 06 nicklas 663       description="Mean of the raw pixel intensity (Integral/Area)"
2959 27 Nov 06 nicklas 664       >
2959 27 Nov 06 nicklas 665       <formula 
2959 27 Nov 06 nicklas 666         channel="1"
2959 27 Nov 06 nicklas 667         expression="raw('ch1Mean')"
2959 27 Nov 06 nicklas 668       />
2959 27 Nov 06 nicklas 669       <formula 
2959 27 Nov 06 nicklas 670         channel="2"
2959 27 Nov 06 nicklas 671         expression="raw('ch2Mean')"
2959 27 Nov 06 nicklas 672       />
2959 27 Nov 06 nicklas 673     </intensity-formula>
2959 27 Nov 06 nicklas 674     <intensity-formula
2959 27 Nov 06 nicklas 675       name="median"
2959 27 Nov 06 nicklas 676       title="Median"
2959 27 Nov 06 nicklas 677       description="Median of the raw pixel intensity"
2959 27 Nov 06 nicklas 678       >
2959 27 Nov 06 nicklas 679       <formula 
2959 27 Nov 06 nicklas 680         channel="1"
2959 27 Nov 06 nicklas 681         expression="raw('ch1Median')"
2959 27 Nov 06 nicklas 682       />
2959 27 Nov 06 nicklas 683       <formula 
2959 27 Nov 06 nicklas 684         channel="2"
2959 27 Nov 06 nicklas 685         expression="raw('ch2Median')"
2959 27 Nov 06 nicklas 686       />
2959 27 Nov 06 nicklas 687     </intensity-formula>
2959 27 Nov 06 nicklas 688   </raw-data-type>
3820 12 Oct 07 nicklas 689
2959 27 Nov 06 nicklas 690   <raw-data-type
2959 27 Nov 06 nicklas 691     id="agilent"
2959 27 Nov 06 nicklas 692     channels="2"
2959 27 Nov 06 nicklas 693     name="Agilent"
2959 27 Nov 06 nicklas 694     table="RawDataAgilent"
2959 27 Nov 06 nicklas 695     >
2959 27 Nov 06 nicklas 696     <property
2959 27 Nov 06 nicklas 697       name="LogRatio"
2959 27 Nov 06 nicklas 698       title="Log ratio"
2959 27 Nov 06 nicklas 699       description="log(REDsignal/GREENsignal) per feature. Signals in both channels are post dye normalization. If SURROGATES are disabled, then this value will be set to: -2 if DyeNormRedSig &lt;= 0.0 amp; DyeNormGreenSig &gt; 0.0; 2 if DyeNormRedSig &gt; 0.0 &amp; DyeNormGreenSig &lt;= 0.0; and 0 if DyeNormRedSig &lt;= 0.0 amp; DyeNormGreenSig &lt;= 0.0."
2959 27 Nov 06 nicklas 700       column="log_ratio"
2959 27 Nov 06 nicklas 701       type="float"
4027 30 Nov 07 enell 702       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 703     />
2959 27 Nov 06 nicklas 704     <property
2959 27 Nov 06 nicklas 705       name="PValueLogRatio"
2959 27 Nov 06 nicklas 706       title="P value log ratio"
2959 27 Nov 06 nicklas 707       description="Significance level of the Log Ratio computed for a feature."
2959 27 Nov 06 nicklas 708       column="pvalue_log_ratio"
2959 27 Nov 06 nicklas 709       type="float"
4027 30 Nov 07 enell 710       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 711     />
2959 27 Nov 06 nicklas 712     <property
2959 27 Nov 06 nicklas 713       name="gSurrogateUsed"
2959 27 Nov 06 nicklas 714       title="G surrogate used"
2959 27 Nov 06 nicklas 715       description="The green surrogate value used."
2959 27 Nov 06 nicklas 716       column="g_surrogate_used"
2959 27 Nov 06 nicklas 717       channel="1"
2959 27 Nov 06 nicklas 718       type="float"
4027 30 Nov 07 enell 719       averagemethod="none"
2959 27 Nov 06 nicklas 720     />
2959 27 Nov 06 nicklas 721     <property
2959 27 Nov 06 nicklas 722       name="rSurrogateUsed"
2959 27 Nov 06 nicklas 723       title="R surrogate used"
2959 27 Nov 06 nicklas 724       description="The red surrogate value used."
2959 27 Nov 06 nicklas 725       column="r_surrogate_used"
2959 27 Nov 06 nicklas 726       channel="2"
2959 27 Nov 06 nicklas 727       type="float"
4027 30 Nov 07 enell 728       averagemethod="none"
2959 27 Nov 06 nicklas 729     />
2959 27 Nov 06 nicklas 730     <property
2959 27 Nov 06 nicklas 731       name="gIsFound"
2959 27 Nov 06 nicklas 732       title="G is found"
2959 27 Nov 06 nicklas 733       description="A boolean used to flag found (strong) features. The flag is applied independently in each channel. A feature is considered found if the found spot centroid is within the bounds of the spot deviation limit with respect to corresponding nominal centroid. NOTE: IsFound was previously termed IsStrong."
2959 27 Nov 06 nicklas 734       column="g_is_found"
2959 27 Nov 06 nicklas 735       channel="1"
2959 27 Nov 06 nicklas 736       type="boolean"
4027 30 Nov 07 enell 737       averagemethod="none"
2959 27 Nov 06 nicklas 738     />
2959 27 Nov 06 nicklas 739     <property
2959 27 Nov 06 nicklas 740       name="rIsFound"
2959 27 Nov 06 nicklas 741       title="R is found"
2959 27 Nov 06 nicklas 742       description="A boolean used to flag found (strong) features. The flag is applied independently in each channel. A feature is considered found if the found spot centroid is within the bounds of the spot deviation limit with respect to corresponding nominal centroid. NOTE: IsFound was previously termed IsStrong."
2959 27 Nov 06 nicklas 743       column="r_is_found"
2959 27 Nov 06 nicklas 744       channel="2"
2959 27 Nov 06 nicklas 745       type="boolean"
4027 30 Nov 07 enell 746       averagemethod="none"
2959 27 Nov 06 nicklas 747     />
2959 27 Nov 06 nicklas 748     <property
2959 27 Nov 06 nicklas 749       name="gProcessedSignal"
2959 27 Nov 06 nicklas 750       title="G processed signal"
2959 27 Nov 06 nicklas 751       description="The propagated feature signal, per channel, used for computation of log ratio."
2959 27 Nov 06 nicklas 752       column="g_processed_signal"
2959 27 Nov 06 nicklas 753       channel="1"
2959 27 Nov 06 nicklas 754       type="float"
4027 30 Nov 07 enell 755       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 756     />
2959 27 Nov 06 nicklas 757     <property
2959 27 Nov 06 nicklas 758       name="rProcessedSignal"
2959 27 Nov 06 nicklas 759       title="R processed signal"
2959 27 Nov 06 nicklas 760       description="The propagated feature signal, per channel, used for computation of log ratio."
2959 27 Nov 06 nicklas 761       column="r_processed_signal"
2959 27 Nov 06 nicklas 762       channel="2"
2959 27 Nov 06 nicklas 763       type="float"
4027 30 Nov 07 enell 764       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 765     />
2959 27 Nov 06 nicklas 766     <property
2959 27 Nov 06 nicklas 767       name="gNumPixOLHi"
2959 27 Nov 06 nicklas 768       title="G high outlier pixels"
2959 27 Nov 06 nicklas 769       description="Number of outlier pixels per feature with intensity &gt; upper threshold set via the pixel outlier rejection method. The number is computed independently in each channel. These pixels are omitted from all subsequent calculations."
2959 27 Nov 06 nicklas 770       column="g_high_outlier_pixels"
2959 27 Nov 06 nicklas 771       channel="1"
2959 27 Nov 06 nicklas 772       type="int"
4027 30 Nov 07 enell 773       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 774     />
2959 27 Nov 06 nicklas 775     <property
2959 27 Nov 06 nicklas 776       name="rNumPixOLHi"
2959 27 Nov 06 nicklas 777       title="R high outlier pixels"
2959 27 Nov 06 nicklas 778       description="Number of outlier pixels per feature with intensity &gt; upper threshold set via the pixel outlier rejection method. The number is computed independently in each channel. These pixels are omitted from all subsequent calculations."
2959 27 Nov 06 nicklas 779       column="r_high_outlier_pixels"
2959 27 Nov 06 nicklas 780       channel="2"
2959 27 Nov 06 nicklas 781       type="int"
4027 30 Nov 07 enell 782       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 783     />
2959 27 Nov 06 nicklas 784     <property
2959 27 Nov 06 nicklas 785       name="gNumPixOLLo"
2959 27 Nov 06 nicklas 786       title="G low outlier pixels"
2959 27 Nov 06 nicklas 787       description="Number of outlier pixels per feature with intensity &lt; lower threshold set via the pixel outlier rejection method. The number is computed independently in each channel. NOTE: The pixel outlier method is the ONLY step that removes data in Feature Extraction."
2959 27 Nov 06 nicklas 788       column="g_low_outlier_pixels"
2959 27 Nov 06 nicklas 789       channel="1"
2959 27 Nov 06 nicklas 790       type="int"
4027 30 Nov 07 enell 791       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 792     />
2959 27 Nov 06 nicklas 793     <property
2959 27 Nov 06 nicklas 794       name="rNumPixOLLo"
2959 27 Nov 06 nicklas 795       title="R low outlier pixels"
2959 27 Nov 06 nicklas 796       description="Number of outlier pixels per feature with intensity &lt; lower threshold set via the pixel outlier rejection method. The number is computed independently in each channel. NOTE: The pixel outlier method is the ONLY step that removes data in Feature Extraction."
2959 27 Nov 06 nicklas 797       column="r_low_outlier_pixels"
2959 27 Nov 06 nicklas 798       channel="2"
2959 27 Nov 06 nicklas 799       type="int"
4027 30 Nov 07 enell 800       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 801     />
2959 27 Nov 06 nicklas 802     <property
2959 27 Nov 06 nicklas 803       name="gNumPix"
2959 27 Nov 06 nicklas 804       title="G pixels"
2959 27 Nov 06 nicklas 805       description="Total number of pixels used to compute feature statistics; ie. total number of inlier pixels/per spot, computed independently in each channel. The number of inlier pixels are the same in both channels."
2959 27 Nov 06 nicklas 806       column="g_pixels"
2959 27 Nov 06 nicklas 807       channel="1"
2959 27 Nov 06 nicklas 808       type="int"
4027 30 Nov 07 enell 809       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 810     />
2959 27 Nov 06 nicklas 811     <property
2959 27 Nov 06 nicklas 812       name="rNumPix"
2959 27 Nov 06 nicklas 813       title="R pixels"
2959 27 Nov 06 nicklas 814       description="Total number of pixels used to compute feature statistics; ie. total number of inlier pixels/per spot, computed independently in each channel. The number of inlier pixels are the same in both channels."
2959 27 Nov 06 nicklas 815       column="r_pixels"
2959 27 Nov 06 nicklas 816       channel="2"
2959 27 Nov 06 nicklas 817       type="int"
4027 30 Nov 07 enell 818       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 819     />
2959 27 Nov 06 nicklas 820     <property
2959 27 Nov 06 nicklas 821       name="gMeanSignal"
2959 27 Nov 06 nicklas 822       title="G mean signal"
2959 27 Nov 06 nicklas 823       description="Raw mean signal of feature in green channel."
2959 27 Nov 06 nicklas 824       column="g_mean_signal"
2959 27 Nov 06 nicklas 825       channel="1"
2959 27 Nov 06 nicklas 826       type="float"
4027 30 Nov 07 enell 827       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 828     />
2959 27 Nov 06 nicklas 829     <property
2959 27 Nov 06 nicklas 830       name="rMeanSignal"
2959 27 Nov 06 nicklas 831       title="R mean signal"
2959 27 Nov 06 nicklas 832       description="Raw mean signal of feature in red channel."
2959 27 Nov 06 nicklas 833       column="r_mean_signal"
2959 27 Nov 06 nicklas 834       channel="2"
2959 27 Nov 06 nicklas 835       type="float"
4027 30 Nov 07 enell 836       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 837     />
2959 27 Nov 06 nicklas 838     <property
2959 27 Nov 06 nicklas 839       name="gMedianSignal"
2959 27 Nov 06 nicklas 840       title="G median signal"
2959 27 Nov 06 nicklas 841       description="Raw median signal of feature in green channel."
2959 27 Nov 06 nicklas 842       column="g_median_signal"
2959 27 Nov 06 nicklas 843       channel="1"
2959 27 Nov 06 nicklas 844       type="float"
4027 30 Nov 07 enell 845       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 846     />
2959 27 Nov 06 nicklas 847     <property
2959 27 Nov 06 nicklas 848       name="rMedianSignal"
2959 27 Nov 06 nicklas 849       title="R median signal"
2959 27 Nov 06 nicklas 850       description="Raw median signal of feature in red channel."
2959 27 Nov 06 nicklas 851       column="r_median_signal"
2959 27 Nov 06 nicklas 852       channel="2"
2959 27 Nov 06 nicklas 853       type="float"
4027 30 Nov 07 enell 854       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 855     />
2959 27 Nov 06 nicklas 856     <property
2959 27 Nov 06 nicklas 857       name="gBGNumPix"
2959 27 Nov 06 nicklas 858       title="G background pixels"
2959 27 Nov 06 nicklas 859       description="Total number of pixels used to compute Local BG statistics per spot; ie. Total number of BG inlier pixels. This number is computed independently in each channel."
2959 27 Nov 06 nicklas 860       column="g_bg_pixels"
2959 27 Nov 06 nicklas 861       channel="1"
2959 27 Nov 06 nicklas 862       type="int"
4027 30 Nov 07 enell 863       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 864     />
2959 27 Nov 06 nicklas 865     <property
2959 27 Nov 06 nicklas 866       name="rBGNumPix"
2959 27 Nov 06 nicklas 867       title="R background pixels"
2959 27 Nov 06 nicklas 868       description="Total number of pixels used to compute Local BG statistics per spot; ie. Total number of BG inlier pixels. This number is computed independently in each channel."
2959 27 Nov 06 nicklas 869       column="r_bg_pixels"
2959 27 Nov 06 nicklas 870       channel="2"
2959 27 Nov 06 nicklas 871       type="int"
4027 30 Nov 07 enell 872       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 873     />
2959 27 Nov 06 nicklas 874     <property
2959 27 Nov 06 nicklas 875       name="gBGMeanSignal"
2959 27 Nov 06 nicklas 876       title="G mean background"
2959 27 Nov 06 nicklas 877       description="Mean local background signal (local to corresponding feature) computed per channel."
2959 27 Nov 06 nicklas 878       column="g_bg_mean_signal"
2959 27 Nov 06 nicklas 879       channel="1"
2959 27 Nov 06 nicklas 880       type="float"
4027 30 Nov 07 enell 881       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 882     />
2959 27 Nov 06 nicklas 883     <property
2959 27 Nov 06 nicklas 884       name="rBGMeanSignal"
2959 27 Nov 06 nicklas 885       title="R mean background"
2959 27 Nov 06 nicklas 886       description="Mean local background signal (local to corresponding feature) computed per channel."
2959 27 Nov 06 nicklas 887       column="r_bg_mean_signal"
2959 27 Nov 06 nicklas 888       channel="2"
2959 27 Nov 06 nicklas 889       type="float"
4027 30 Nov 07 enell 890       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 891     />
2959 27 Nov 06 nicklas 892     <property
2959 27 Nov 06 nicklas 893       name="gBGMedianSignal"
2959 27 Nov 06 nicklas 894       title="G median background"
2959 27 Nov 06 nicklas 895       description="Median local background signal (local to corresponding feature) computed per channel."
2959 27 Nov 06 nicklas 896       column="g_bg_median_signal"
2959 27 Nov 06 nicklas 897       channel="1"
2959 27 Nov 06 nicklas 898       type="float"
4027 30 Nov 07 enell 899       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 900     />
2959 27 Nov 06 nicklas 901     <property
2959 27 Nov 06 nicklas 902       name="rBGMedianSignal"
2959 27 Nov 06 nicklas 903       title="R median background"
2959 27 Nov 06 nicklas 904       description="Median local background signal (local to corresponding feature) computed per channel."
2959 27 Nov 06 nicklas 905       column="r_bg_median_signal"
2959 27 Nov 06 nicklas 906       channel="2"
2959 27 Nov 06 nicklas 907       type="float"
4027 30 Nov 07 enell 908       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 909     />
2959 27 Nov 06 nicklas 910     <property
2959 27 Nov 06 nicklas 911       name="gNumSatPix"
2959 27 Nov 06 nicklas 912       title="G saturated pixels"
2959 27 Nov 06 nicklas 913       description="Total number of saturated pixels per feature, computed per channel."
2959 27 Nov 06 nicklas 914       column="g_sat_pixels"
2959 27 Nov 06 nicklas 915       channel="1"
2959 27 Nov 06 nicklas 916       type="int"
4027 30 Nov 07 enell 917       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 918     />
2959 27 Nov 06 nicklas 919     <property
2959 27 Nov 06 nicklas 920       name="rNumSatPix"
2959 27 Nov 06 nicklas 921       title="R saturated pixels"
2959 27 Nov 06 nicklas 922       description="Total number of saturated pixels per feature, computed per channel."
2959 27 Nov 06 nicklas 923       column="r_sat_pixels"
2959 27 Nov 06 nicklas 924       channel="2"
2959 27 Nov 06 nicklas 925       type="int"
4027 30 Nov 07 enell 926       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 927     />
2959 27 Nov 06 nicklas 928     <property
2959 27 Nov 06 nicklas 929       name="gIsSaturated"
2959 27 Nov 06 nicklas 930       title="G is saturated"
2959 27 Nov 06 nicklas 931       description="Boolean flag indicating if a feature is saturated or not. A feature is saturated if 50% of the pixels in a feature are above the saturation threshold. A value of 1 means saturated."
2959 27 Nov 06 nicklas 932       column="g_is_saturated"
2959 27 Nov 06 nicklas 933       channel="1"
2959 27 Nov 06 nicklas 934       type="boolean"
4027 30 Nov 07 enell 935       averagemethod="none"
2959 27 Nov 06 nicklas 936     />
2959 27 Nov 06 nicklas 937     <property
2959 27 Nov 06 nicklas 938       name="rIsSaturated"
2959 27 Nov 06 nicklas 939       title="R is saturated"
2959 27 Nov 06 nicklas 940       description="Boolean flag indicating if a feature is saturated or not. A feature is saturated if 50% of the pixels in a feature are above the saturation threshold. A value of 1 means saturated."
2959 27 Nov 06 nicklas 941       column="r_is_saturated"
2959 27 Nov 06 nicklas 942       channel="2"
2959 27 Nov 06 nicklas 943       type="boolean"
4027 30 Nov 07 enell 944       averagemethod="none"
2959 27 Nov 06 nicklas 945     />
2959 27 Nov 06 nicklas 946     <property
2959 27 Nov 06 nicklas 947       name="PixCorrelation"
2959 27 Nov 06 nicklas 948       title="Pix correlation"
2959 27 Nov 06 nicklas 949       description="Ratio of estimated feature covariance in RedGreen space to product of feature Standard Deviation in Red Green space. The covariance of two features measures their tendency to vary together, i.e. to co-vary. In this case, it is a cumulative quantitation of the tendency of pixels belonging to a particular feature in Red and Green spaces to co-vary."
2959 27 Nov 06 nicklas 950       column="pix_correlation"
2959 27 Nov 06 nicklas 951       type="float"
4027 30 Nov 07 enell 952       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 953     />
2959 27 Nov 06 nicklas 954     <property
2959 27 Nov 06 nicklas 955       name="BGPixCorrelation"
2959 27 Nov 06 nicklas 956       title="BG pix correlation"
2959 27 Nov 06 nicklas 957       description="Ratio of estimated feature covariance in RedGreen space to product of feature Standard Deviation in Red Green space. The covariance of two features measures their tendency to vary together, i.e. to co-vary. In this case, it is a cumulative quantitation of the tendency of pixels belonging to a particular feature in Red and Green spaces to co-vary."
2959 27 Nov 06 nicklas 958       column="bg_pix_correlation"
2959 27 Nov 06 nicklas 959       type="float"
4027 30 Nov 07 enell 960       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 961     />
2959 27 Nov 06 nicklas 962     <property
2959 27 Nov 06 nicklas 963       name="gIsFeatNonUnifOL"
2959 27 Nov 06 nicklas 964       title="G non-uniform outlier"
2959 27 Nov 06 nicklas 965       description="Boolean flag indicating if a feature is a NonUniformity Outlier or not. A feature is non-uniform if the pixel noise of feature exceeds a threshold established for a 'uniform' feature. A 1 indicates Feature is a non-uniformity outlier."
2959 27 Nov 06 nicklas 966       column="g_nonuniform_outlier"
2959 27 Nov 06 nicklas 967       channel="1"
2959 27 Nov 06 nicklas 968       type="boolean"
4027 30 Nov 07 enell 969       averagemethod="none"
2959 27 Nov 06 nicklas 970     />
2959 27 Nov 06 nicklas 971     <property
2959 27 Nov 06 nicklas 972       name="rIsFeatNonUnifOL"
2959 27 Nov 06 nicklas 973       title="R non-uniform outlier"
2959 27 Nov 06 nicklas 974       description="Boolean flag indicating if a feature is a NonUniformity Outlier or not. A feature is non-uniform if the pixel noise of feature exceeds a threshold established for a 'uniform' feature. A 1 indicates Feature is a non-uniformity outlier."
2959 27 Nov 06 nicklas 975       column="r_nonuniform_outlier"
2959 27 Nov 06 nicklas 976       channel="2"
2959 27 Nov 06 nicklas 977       type="boolean"
2959 27 Nov 06 nicklas 978     />
2959 27 Nov 06 nicklas 979     <property
2959 27 Nov 06 nicklas 980       name="gIsBGNonUnifOL"
2959 27 Nov 06 nicklas 981       title="G bg non-uniform outlier"
2959 27 Nov 06 nicklas 982       description="Boolean flag indicating if a background is a NonUniformity Outlier or not. A feature is non-uniform if the pixel noise of feature exceeds a threshold established for a 'uniform' feature. A 1 indicates Feature is a non-uniformity outlier."
2959 27 Nov 06 nicklas 983       column="g_bg_nonuniform_outlier"
2959 27 Nov 06 nicklas 984       channel="1"
2959 27 Nov 06 nicklas 985       type="boolean"
2959 27 Nov 06 nicklas 986     />
2959 27 Nov 06 nicklas 987     <property
2959 27 Nov 06 nicklas 988       name="rIsBGNonUnifOL"
2959 27 Nov 06 nicklas 989       title="R bg non-uniform outlier"
2959 27 Nov 06 nicklas 990       description="Boolean flag indicating if a background is a NonUniformity Outlier or not. A feature is non-uniform if the pixel noise of feature exceeds a threshold established for a 'uniform' feature. A 1 indicates Feature is a non-uniformity outlier."
2959 27 Nov 06 nicklas 991       column="r_bg_nonuniform_outlier"
2959 27 Nov 06 nicklas 992       channel="2"
2959 27 Nov 06 nicklas 993       type="boolean"
2959 27 Nov 06 nicklas 994     />
2959 27 Nov 06 nicklas 995     <property
2959 27 Nov 06 nicklas 996       name="gIsFeatPopnOL"
2959 27 Nov 06 nicklas 997       title="G population outlier"
2959 27 Nov 06 nicklas 998       description="Boolean flag indicating if a feature is a Population Outlier or not. Probes with replicate features on a microarray are examined using population statistics. A feature is a population outlier if its signal is less than a lower threshold or exceeds an upper threshold determined using the interquartile range (i.e. IQR) of the population. A 1 indicates Feature is a population outlier."
2959 27 Nov 06 nicklas 999       column="g_population_outlier"
2959 27 Nov 06 nicklas 1000       channel="1"
2959 27 Nov 06 nicklas 1001       type="boolean"
2959 27 Nov 06 nicklas 1002     />
2959 27 Nov 06 nicklas 1003     <property
2959 27 Nov 06 nicklas 1004       name="rIsFeatPopnOL"
2959 27 Nov 06 nicklas 1005       title="R population outlier"
2959 27 Nov 06 nicklas 1006       description="Boolean flag indicating if a feature is a Population Outlier or not. Probes with replicate features on a microarray are examined using population statistics. A feature is a population outlier if its signal is less than a lower threshold or exceeds an upper threshold determined using the interquartile range (i.e. IQR) of the population. A 1 indicates Feature is a population outlier."
2959 27 Nov 06 nicklas 1007       column="r_population_outlier"
2959 27 Nov 06 nicklas 1008       channel="2"
2959 27 Nov 06 nicklas 1009       type="boolean"
4027 30 Nov 07 enell 1010       averagemethod="none"
2959 27 Nov 06 nicklas 1011     />
2959 27 Nov 06 nicklas 1012     <property
2959 27 Nov 06 nicklas 1013       name="gIsBGPopnOL"
2959 27 Nov 06 nicklas 1014       title="G bg population outlier"
2959 27 Nov 06 nicklas 1015       description="Boolean flag indicating if a background is a Population Outlier or not. Probes with replicate features on a microarray are examined using population statistics. A feature is a population outlier if its signal is less than a lower threshold or exceeds an upper threshold determined using the interquartile range (i.e. IQR) of the population. A 1 indicates background is a population outlier."
2959 27 Nov 06 nicklas 1016       column="g_bg_population_outlier"
2959 27 Nov 06 nicklas 1017       channel="1"
2959 27 Nov 06 nicklas 1018       type="boolean"
4027 30 Nov 07 enell 1019       averagemethod="none"
2959 27 Nov 06 nicklas 1020     />
2959 27 Nov 06 nicklas 1021     <property
2959 27 Nov 06 nicklas 1022       name="rIsBGPopnOL"
2959 27 Nov 06 nicklas 1023       title="R bg population outlier"
2959 27 Nov 06 nicklas 1024       description="Boolean flag indicating if a background is a Population Outlier or not. Probes with replicate features on a microarray are examined using population statistics. A feature is a population outlier if its signal is less than a lower threshold or exceeds an upper threshold determined using the interquartile range (i.e. IQR) of the population. A 1 indicates background is a population outlier."
2959 27 Nov 06 nicklas 1025       column="r_bg_population_outlier"
2959 27 Nov 06 nicklas 1026       channel="2"
2959 27 Nov 06 nicklas 1027       type="boolean"
4027 30 Nov 07 enell 1028       averagemethod="none"
2959 27 Nov 06 nicklas 1029     />
2959 27 Nov 06 nicklas 1030     <property
2959 27 Nov 06 nicklas 1031       name="IsManualFlag"
2959 27 Nov 06 nicklas 1032       title="Manual flag"
2959 27 Nov 06 nicklas 1033       description="If a feature has been moved manually this flag will be set to 1."
2959 27 Nov 06 nicklas 1034       column="manual_flag"
2959 27 Nov 06 nicklas 1035       type="boolean"
4027 30 Nov 07 enell 1036       averagemethod="none"
2959 27 Nov 06 nicklas 1037     />
2959 27 Nov 06 nicklas 1038     <property
2959 27 Nov 06 nicklas 1039       name="gBGSubSignal"
2959 27 Nov 06 nicklas 1040       title="G net signal"
2959 27 Nov 06 nicklas 1041       description="The net green signal following the subtraction of the background from the raw mean green signal."
2959 27 Nov 06 nicklas 1042       column="g_net_signal"
2959 27 Nov 06 nicklas 1043       channel="1"
2959 27 Nov 06 nicklas 1044       type="float"
2959 27 Nov 06 nicklas 1045     />
2959 27 Nov 06 nicklas 1046     <property
2959 27 Nov 06 nicklas 1047       name="rBGSubSignal"
2959 27 Nov 06 nicklas 1048       title="R net signal"
2959 27 Nov 06 nicklas 1049       description="The net red signal following the subtraction of the background from the raw mean red signal."
2959 27 Nov 06 nicklas 1050       column="r_net_signal"
2959 27 Nov 06 nicklas 1051       channel="2"
2959 27 Nov 06 nicklas 1052       type="float"
4027 30 Nov 07 enell 1053       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1054     />
2959 27 Nov 06 nicklas 1055     <property
2959 27 Nov 06 nicklas 1056       name="BGSubSigCorrelation"
2959 27 Nov 06 nicklas 1057       title="BG correlation"
2959 27 Nov 06 nicklas 1058       description="Ratio of estimated background subtracted feature signal covariance in RG space to product of background subtracted feature Standard Deviation in RG space."
2959 27 Nov 06 nicklas 1059       column="bg_correlation"
2959 27 Nov 06 nicklas 1060       type="float"
4027 30 Nov 07 enell 1061       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 1062     />
2959 27 Nov 06 nicklas 1063     <property
2959 27 Nov 06 nicklas 1064       name="gIsPosAndSignif"
2959 27 Nov 06 nicklas 1065       title="G > 0 and significant"
2959 27 Nov 06 nicklas 1066       description="Boolean flag indicating if the mean signal of a feature is greater than the corresponding background and if this difference is significant. Significance is established via a 2-sided t-test against the user-settable maximum p-value. A 1 indicates Feature is positive and significant above background."
2959 27 Nov 06 nicklas 1067       column="g_significant"
2959 27 Nov 06 nicklas 1068       channel="1"
2959 27 Nov 06 nicklas 1069       type="boolean"
4027 30 Nov 07 enell 1070       averagemethod="none"
2959 27 Nov 06 nicklas 1071     />
2959 27 Nov 06 nicklas 1072     <property
2959 27 Nov 06 nicklas 1073       name="rIsPosAndSignif"
2959 27 Nov 06 nicklas 1074       title="R > 0 and significant"
2959 27 Nov 06 nicklas 1075       description="Boolean flag indicating if the mean signal of a feature is greater than the corresponding background and if this difference is significant. Significance is established via a 2-sided t-test against the user-settable maximum p-value. A 1 indicates Feature is positive and significant above background."
2959 27 Nov 06 nicklas 1076       column="r_significant"
2959 27 Nov 06 nicklas 1077       channel="2"
2959 27 Nov 06 nicklas 1078       type="boolean"
4027 30 Nov 07 enell 1079       averagemethod="none"
2959 27 Nov 06 nicklas 1080     />
2959 27 Nov 06 nicklas 1081     <property
2959 27 Nov 06 nicklas 1082       name="gPValFeatEqBG"
2959 27 Nov 06 nicklas 1083       title="G p-value"
2959 27 Nov 06 nicklas 1084       description="P-value from t-test of significance between green Mean signal and green background."
2959 27 Nov 06 nicklas 1085       column="g_pvalue"
2959 27 Nov 06 nicklas 1086       channel="1"
2959 27 Nov 06 nicklas 1087       type="float"
4027 30 Nov 07 enell 1088       averagemethod="none"
2959 27 Nov 06 nicklas 1089     />
2959 27 Nov 06 nicklas 1090     <property
2959 27 Nov 06 nicklas 1091       name="rPValFeatEqBG"
2959 27 Nov 06 nicklas 1092       title="R p-value"
2959 27 Nov 06 nicklas 1093       description="P-value from t-test of significance between red Mean signal and red background."
2959 27 Nov 06 nicklas 1094       column="r_pvalue"
2959 27 Nov 06 nicklas 1095       channel="2"
2959 27 Nov 06 nicklas 1096       type="float"
4027 30 Nov 07 enell 1097       averagemethod="none"
2959 27 Nov 06 nicklas 1098     />
2959 27 Nov 06 nicklas 1099     <property
2959 27 Nov 06 nicklas 1100       name="gNumBGUsed"
2959 27 Nov 06 nicklas 1101       title="G background pixels"
2959 27 Nov 06 nicklas 1102       description="A count of the number of background pixels used in the green channel."
2959 27 Nov 06 nicklas 1103       column="g_numbg_used"
2959 27 Nov 06 nicklas 1104       channel="1"
2959 27 Nov 06 nicklas 1105       type="int"
4027 30 Nov 07 enell 1106       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1107     />
2959 27 Nov 06 nicklas 1108     <property
2959 27 Nov 06 nicklas 1109       name="rNumBGUsed"
2959 27 Nov 06 nicklas 1110       title="R background pixels"
2959 27 Nov 06 nicklas 1111       description="A count of the number of background pixels used in the red channel."
2959 27 Nov 06 nicklas 1112       column="r_numbg_used"
2959 27 Nov 06 nicklas 1113       channel="2"
2959 27 Nov 06 nicklas 1114       type="int"
4027 30 Nov 07 enell 1115       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1116     />
2959 27 Nov 06 nicklas 1117     <property
2959 27 Nov 06 nicklas 1118       name="gIsWellAboveBG"
2959 27 Nov 06 nicklas 1119       title="G well above bg"
2959 27 Nov 06 nicklas 1120       description="Boolean flag indicating if a feature is well above background or not. A feature must be gIsPosAndSignif and additionally the gBGSubSignal must be greater than 2.6*g(r)BG_SD. A 1 indicates a feature IsWellAboveBG."
2959 27 Nov 06 nicklas 1121       column="g_above_bg"
2959 27 Nov 06 nicklas 1122       channel="1"
2959 27 Nov 06 nicklas 1123       type="boolean"
4027 30 Nov 07 enell 1124       averagemethod="none"
2959 27 Nov 06 nicklas 1125     />
2959 27 Nov 06 nicklas 1126     <property
2959 27 Nov 06 nicklas 1127       name="rIsWellAboveBG"
2959 27 Nov 06 nicklas 1128       title="R well above bg"
2959 27 Nov 06 nicklas 1129       description="Boolean flag indicating if a feature is well above background or not. A feature must be gIsPosAndSignif and additionally the gBGSubSignal must be greater than 2.6*g(r)BG_SD. A 1 indicates a feature IsWellAboveBG."
2959 27 Nov 06 nicklas 1130       column="r_above_bg"
2959 27 Nov 06 nicklas 1131       channel="2"
2959 27 Nov 06 nicklas 1132       type="boolean"
4027 30 Nov 07 enell 1133       averagemethod="none"
2959 27 Nov 06 nicklas 1134     />
2959 27 Nov 06 nicklas 1135     <property
2959 27 Nov 06 nicklas 1136       name="gBGUsed"
2959 27 Nov 06 nicklas 1137       title="G bg used"
2959 27 Nov 06 nicklas 1138       description="Background value subtracted from the raw mean signal to generate the BG subtracted signal; this value is computed per channel. If global BG subtraction is used the column is identical for every feature in a given channel."
2959 27 Nov 06 nicklas 1139       column="g_bg_used"
2959 27 Nov 06 nicklas 1140       channel="1"
2959 27 Nov 06 nicklas 1141       type="float"
4027 30 Nov 07 enell 1142       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1143     />
2959 27 Nov 06 nicklas 1144     <property
2959 27 Nov 06 nicklas 1145       name="rBGUsed"
2959 27 Nov 06 nicklas 1146       title="R bg used"
2959 27 Nov 06 nicklas 1147       description="Background value subtracted from the raw mean signal to generate the BG subtracted signal; this value is computed per channel. If global BG subtraction is used the column is identical for every feature in a given channel."
2959 27 Nov 06 nicklas 1148       column="r_bg_used"
2959 27 Nov 06 nicklas 1149       channel="2"
2959 27 Nov 06 nicklas 1150       type="float"
4027 30 Nov 07 enell 1151       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1152     />
2959 27 Nov 06 nicklas 1153     <property
2959 27 Nov 06 nicklas 1154       name="IsNormalization"
2959 27 Nov 06 nicklas 1155       title="Normalization"
2959 27 Nov 06 nicklas 1156       description="A boolean flag which indicates if a feature is used to measure dye bias. A 1 incidates the value was used."
2959 27 Nov 06 nicklas 1157       column="is_normalization"
2959 27 Nov 06 nicklas 1158       type="boolean"
4027 30 Nov 07 enell 1159       averagemethod="none"
2959 27 Nov 06 nicklas 1160     />
2959 27 Nov 06 nicklas 1161     <property
2959 27 Nov 06 nicklas 1162       name="gDyeNormSignal"
2959 27 Nov 06 nicklas 1163       title="G normalized signal"
2959 27 Nov 06 nicklas 1164       description="The dye normalized signal in the green channel."
2959 27 Nov 06 nicklas 1165       column="g_normalized"
2959 27 Nov 06 nicklas 1166       channel="1"
2959 27 Nov 06 nicklas 1167       type="float"
4027 30 Nov 07 enell 1168       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1169     />
2959 27 Nov 06 nicklas 1170     <property
2959 27 Nov 06 nicklas 1171       name="rDyeNormSignal"
2959 27 Nov 06 nicklas 1172       title="R normalized signal"
2959 27 Nov 06 nicklas 1173       description="The dye normalized signal in the green channel."
2959 27 Nov 06 nicklas 1174       column="r_normalized"
2959 27 Nov 06 nicklas 1175       channel="2"
2959 27 Nov 06 nicklas 1176       type="float"
4027 30 Nov 07 enell 1177       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1178     />
2959 27 Nov 06 nicklas 1179     <property
2959 27 Nov 06 nicklas 1180       name="DyeNormCorrelation"
2959 27 Nov 06 nicklas 1181       title="Normalized correlation"
2959 27 Nov 06 nicklas 1182       description="Dye normalized red and green pixel correlation."
2959 27 Nov 06 nicklas 1183       column="norm_correlation"
2959 27 Nov 06 nicklas 1184       type="float"
4027 30 Nov 07 enell 1185       averagemethod="none"
2959 27 Nov 06 nicklas 1186     />
2959 27 Nov 06 nicklas 1187     <property
2959 27 Nov 06 nicklas 1188       name="ErrorModel"
2959 27 Nov 06 nicklas 1189       title="Error model"
2959 27 Nov 06 nicklas 1190       description="ErrorModel Indicates the error model that the user chose for feature extraction. A 0 indicates use of the Propogated Error Model. A 1 indicates use of the Universal Error Model."
2959 27 Nov 06 nicklas 1191       column="error_model"
2959 27 Nov 06 nicklas 1192       type="int"
4027 30 Nov 07 enell 1193       averagemethod="none"
2959 27 Nov 06 nicklas 1194     />
2959 27 Nov 06 nicklas 1195     <property
2959 27 Nov 06 nicklas 1196       name="xDev"
2959 27 Nov 06 nicklas 1197       title="X dev"
2959 27 Nov 06 nicklas 1198       description="Used to compute the Log Ratio PValue."
2959 27 Nov 06 nicklas 1199       column="x_dev"
2959 27 Nov 06 nicklas 1200       type="float"
4027 30 Nov 07 enell 1201       averagemethod="none"
2959 27 Nov 06 nicklas 1202     />
2959 27 Nov 06 nicklas 1203     <property
2959 27 Nov 06 nicklas 1204       name="gSpatialDetrendIsInFilteredSet"
2959 27 Nov 06 nicklas 1205       title="G spatial trend"
2959 27 Nov 06 nicklas 1206       description="Set to true for a given feature if it is part of the filtered set used to fit the surface measuring the spatial trend across the microarray. This feature is considered part of the locally weighted x% of the features."
2959 27 Nov 06 nicklas 1207       column="g_spatial_trend"
2959 27 Nov 06 nicklas 1208       channel="1"
2959 27 Nov 06 nicklas 1209       type="boolean"
4027 30 Nov 07 enell 1210       averagemethod="none"
2959 27 Nov 06 nicklas 1211     />
2959 27 Nov 06 nicklas 1212     <property
2959 27 Nov 06 nicklas 1213       name="rSpatialDetrendIsInFilteredSet"
2959 27 Nov 06 nicklas 1214       title="R spatial trend"
2959 27 Nov 06 nicklas 1215       description="Set to true for a given feature if it is part of the filtered set used to fit the surface measuring the spatial trend across the microarray. This feature is considered part of the locally weighted x% of the features."
2959 27 Nov 06 nicklas 1216       column="r_spatial_trend"
2959 27 Nov 06 nicklas 1217       channel="2"
2959 27 Nov 06 nicklas 1218       type="boolean"
4027 30 Nov 07 enell 1219       averagemethod="none"
2959 27 Nov 06 nicklas 1220     />
2959 27 Nov 06 nicklas 1221     <property
2959 27 Nov 06 nicklas 1222       name="gSpatialDetrendSurfaceValue"
2959 27 Nov 06 nicklas 1223       title="G surface value"
2959 27 Nov 06 nicklas 1224       description="Value of the smoothed surface derived from the set of features that are part of SpatialDetrendIsInFilteredSet."
2959 27 Nov 06 nicklas 1225       column="g_surface_value"
2959 27 Nov 06 nicklas 1226       channel="1"
2959 27 Nov 06 nicklas 1227       type="float"
4027 30 Nov 07 enell 1228       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1229     />
2959 27 Nov 06 nicklas 1230     <property
2959 27 Nov 06 nicklas 1231       name="rSpatialDetrendSurfaceValue"
2959 27 Nov 06 nicklas 1232       title="R surface value"
2959 27 Nov 06 nicklas 1233       description="Value of the smoothed surface derived from the set of features that are part of SpatialDetrendIsInFilteredSet."
2959 27 Nov 06 nicklas 1234       column="r_surface_value"
2959 27 Nov 06 nicklas 1235       channel="2"
2959 27 Nov 06 nicklas 1236       type="float"
4027 30 Nov 07 enell 1237       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1238     />
2959 27 Nov 06 nicklas 1239     <intensity-formula
2959 27 Nov 06 nicklas 1240       name="mean"
2959 27 Nov 06 nicklas 1241       title="Mean FG - Mean BG"
2959 27 Nov 06 nicklas 1242       description="Subtract mean background from mean foreground"
2959 27 Nov 06 nicklas 1243       >
2959 27 Nov 06 nicklas 1244       <formula 
2959 27 Nov 06 nicklas 1245         channel="1"
2959 27 Nov 06 nicklas 1246         expression="raw('gMeanSignal') - raw('gBGMeanSignal')"
2959 27 Nov 06 nicklas 1247       />
2959 27 Nov 06 nicklas 1248       <formula 
2959 27 Nov 06 nicklas 1249         channel="2"
2959 27 Nov 06 nicklas 1250         expression="raw('rMeanSignal') - raw('rBGMeanSignal')"
2959 27 Nov 06 nicklas 1251       />
2959 27 Nov 06 nicklas 1252     </intensity-formula>
2959 27 Nov 06 nicklas 1253     <intensity-formula
2959 27 Nov 06 nicklas 1254       name="median"
2959 27 Nov 06 nicklas 1255       title="Median FG - Median BG"
2959 27 Nov 06 nicklas 1256       description="Subtract meadian background from median foreground"
2959 27 Nov 06 nicklas 1257       >
2959 27 Nov 06 nicklas 1258       <formula 
2959 27 Nov 06 nicklas 1259         channel="1"
2959 27 Nov 06 nicklas 1260         expression="raw('gMedianSignal') - raw('gBGMedianSignal')"
2959 27 Nov 06 nicklas 1261       />
2959 27 Nov 06 nicklas 1262       <formula 
2959 27 Nov 06 nicklas 1263         channel="2"
2959 27 Nov 06 nicklas 1264         expression="raw('rMedianSignal') - raw('rBGMedianSignal')"
2959 27 Nov 06 nicklas 1265       />
2959 27 Nov 06 nicklas 1266     </intensity-formula>
2959 27 Nov 06 nicklas 1267     <intensity-formula
2959 27 Nov 06 nicklas 1268       name="medianmean"
2959 27 Nov 06 nicklas 1269       title="Median FG - Mean BG"
2959 27 Nov 06 nicklas 1270       description="Subtract mean background from median foreground"
2959 27 Nov 06 nicklas 1271       >
2959 27 Nov 06 nicklas 1272       <formula 
2959 27 Nov 06 nicklas 1273         channel="1"
2959 27 Nov 06 nicklas 1274         expression="raw('gMedianSignal') - raw('gBGMeanSignal')"
2959 27 Nov 06 nicklas 1275       />
2959 27 Nov 06 nicklas 1276       <formula 
2959 27 Nov 06 nicklas 1277         channel="2"
2959 27 Nov 06 nicklas 1278         expression="raw('rMedianSignal') - raw('rBGMeanSignal')"
2959 27 Nov 06 nicklas 1279       />
2959 27 Nov 06 nicklas 1280     </intensity-formula>
2959 27 Nov 06 nicklas 1281     <intensity-formula
2959 27 Nov 06 nicklas 1282       name="meanmedian"
2959 27 Nov 06 nicklas 1283       title="Mean FG - Median BG"
2959 27 Nov 06 nicklas 1284       description="Subtract median background from mean foreground"
2959 27 Nov 06 nicklas 1285       >
2959 27 Nov 06 nicklas 1286       <formula 
2959 27 Nov 06 nicklas 1287         channel="1"
2959 27 Nov 06 nicklas 1288         expression="raw('gMeanSignal') - raw('gBGMedianSignal')"
2959 27 Nov 06 nicklas 1289       />
2959 27 Nov 06 nicklas 1290       <formula 
2959 27 Nov 06 nicklas 1291         channel="2"
2959 27 Nov 06 nicklas 1292         expression="raw('rMeanSignal') - raw('rBGMedianSignal')"
2959 27 Nov 06 nicklas 1293       />
2959 27 Nov 06 nicklas 1294     </intensity-formula>
2959 27 Nov 06 nicklas 1295     <intensity-formula
2959 27 Nov 06 nicklas 1296       name="meanfg"
2959 27 Nov 06 nicklas 1297       title="Mean FG"
2959 27 Nov 06 nicklas 1298       description="Mean foreground"
2959 27 Nov 06 nicklas 1299       >
2959 27 Nov 06 nicklas 1300       <formula 
2959 27 Nov 06 nicklas 1301         channel="1"
2959 27 Nov 06 nicklas 1302         expression="raw('gMeanSignal')"
2959 27 Nov 06 nicklas 1303       />
2959 27 Nov 06 nicklas 1304       <formula 
2959 27 Nov 06 nicklas 1305         channel="2"
2959 27 Nov 06 nicklas 1306         expression="raw('rMeanSignal')"
2959 27 Nov 06 nicklas 1307       />
2959 27 Nov 06 nicklas 1308     </intensity-formula>
2959 27 Nov 06 nicklas 1309     <intensity-formula
2959 27 Nov 06 nicklas 1310       name="medianfg"
2959 27 Nov 06 nicklas 1311       title="Median FG"
2959 27 Nov 06 nicklas 1312       description="Median foreground"
2959 27 Nov 06 nicklas 1313       >
2959 27 Nov 06 nicklas 1314       <formula 
2959 27 Nov 06 nicklas 1315         channel="1"
2959 27 Nov 06 nicklas 1316         expression="raw('gMedianSignal')"
2959 27 Nov 06 nicklas 1317       />
2959 27 Nov 06 nicklas 1318       <formula 
2959 27 Nov 06 nicklas 1319         channel="2"
2959 27 Nov 06 nicklas 1320         expression="raw('rMedianSignal')"
2959 27 Nov 06 nicklas 1321       />
2959 27 Nov 06 nicklas 1322     </intensity-formula>
2959 27 Nov 06 nicklas 1323     <intensity-formula
2959 27 Nov 06 nicklas 1324       name="medianfgmeanmedianbg"
2959 27 Nov 06 nicklas 1325       title="Median FG - Mean(Median BG)"
2959 27 Nov 06 nicklas 1326       description="Subtract mean of median backgrounds from median foreground"
2959 27 Nov 06 nicklas 1327       >
2959 27 Nov 06 nicklas 1328       <formula 
2959 27 Nov 06 nicklas 1329         channel="1"
2959 27 Nov 06 nicklas 1330         expression="raw('gMedianSignal') - mean('gBGMedianSignal')"
2959 27 Nov 06 nicklas 1331       />
2959 27 Nov 06 nicklas 1332       <formula 
2959 27 Nov 06 nicklas 1333         channel="2"
2959 27 Nov 06 nicklas 1334         expression="raw('rMedianSignal') - mean('rBGMedianSignal')"
2959 27 Nov 06 nicklas 1335       />
2959 27 Nov 06 nicklas 1336     </intensity-formula>
2959 27 Nov 06 nicklas 1337     <intensity-formula
2959 27 Nov 06 nicklas 1338       name="meanfgmeanmeanbg"
2959 27 Nov 06 nicklas 1339       title="Mean FG - Mean(Mean BG)"
2959 27 Nov 06 nicklas 1340       description="Subtract mean of mean backgrounds from mean foreground"
2959 27 Nov 06 nicklas 1341       >
2959 27 Nov 06 nicklas 1342       <formula 
2959 27 Nov 06 nicklas 1343         channel="1"
2959 27 Nov 06 nicklas 1344         expression="raw('gMeanSignal') - mean('gBGMeanSignal')"
2959 27 Nov 06 nicklas 1345       />
2959 27 Nov 06 nicklas 1346       <formula 
2959 27 Nov 06 nicklas 1347         channel="2"
2959 27 Nov 06 nicklas 1348         expression="raw('rMeanSignal') - mean('rBGMeanSignal')"
2959 27 Nov 06 nicklas 1349       />
2959 27 Nov 06 nicklas 1350     </intensity-formula>
2959 27 Nov 06 nicklas 1351     <intensity-formula
2959 27 Nov 06 nicklas 1352       name="medianfgmeanmeanbg"
2959 27 Nov 06 nicklas 1353       title="Median FG - Mean(Mean BG)"
2959 27 Nov 06 nicklas 1354       description="Subtract mean of mean backgrounds from median foreground"
2959 27 Nov 06 nicklas 1355       >
2959 27 Nov 06 nicklas 1356       <formula 
2959 27 Nov 06 nicklas 1357         channel="1"
2959 27 Nov 06 nicklas 1358         expression="raw('gMedianSignal') - mean('gBGMeanSignal')"
2959 27 Nov 06 nicklas 1359       />
2959 27 Nov 06 nicklas 1360       <formula 
2959 27 Nov 06 nicklas 1361         channel="2"
2959 27 Nov 06 nicklas 1362         expression="raw('rMedianSignal') - mean('rBGMeanSignal')"
2959 27 Nov 06 nicklas 1363       />
2959 27 Nov 06 nicklas 1364     </intensity-formula>
2959 27 Nov 06 nicklas 1365     <intensity-formula
2959 27 Nov 06 nicklas 1366       name="meanfgmeanmedianbg"
2959 27 Nov 06 nicklas 1367       title="Mean FG - Mean(Median BG)"
2959 27 Nov 06 nicklas 1368       description="Subtract mean of median backgrounds from mean foreground"
2959 27 Nov 06 nicklas 1369       >
2959 27 Nov 06 nicklas 1370       <formula 
2959 27 Nov 06 nicklas 1371         channel="1"
2959 27 Nov 06 nicklas 1372         expression="raw('gMeanSignal') - mean('gBGMedianSignal')"
2959 27 Nov 06 nicklas 1373       />
2959 27 Nov 06 nicklas 1374       <formula 
2959 27 Nov 06 nicklas 1375         channel="2"
2959 27 Nov 06 nicklas 1376         expression="raw('rMeanSignal') - mean('rBGMedianSignal')"
2959 27 Nov 06 nicklas 1377       />
2959 27 Nov 06 nicklas 1378     </intensity-formula>
2959 27 Nov 06 nicklas 1379   </raw-data-type>
2959 27 Nov 06 nicklas 1380   
2959 27 Nov 06 nicklas 1381   <raw-data-type
2959 27 Nov 06 nicklas 1382     id="chipskipper"
2959 27 Nov 06 nicklas 1383     channels="2"
2959 27 Nov 06 nicklas 1384     name="ChipSkipper"
2959 27 Nov 06 nicklas 1385     table="RawDataChipSkipper"
2959 27 Nov 06 nicklas 1386     >
2959 27 Nov 06 nicklas 1387     <property
2959 27 Nov 06 nicklas 1388       name="Line_Counter"
2959 27 Nov 06 nicklas 1389       title="Line counter"
2959 27 Nov 06 nicklas 1390       description="Line counter."
2959 27 Nov 06 nicklas 1391       column="line_counter"
2959 27 Nov 06 nicklas 1392       type="int"
4027 30 Nov 07 enell 1393       averagemethod="none"
2959 27 Nov 06 nicklas 1394     />
2959 27 Nov 06 nicklas 1395     <property
2959 27 Nov 06 nicklas 1396       name="Flags"
2959 27 Nov 06 nicklas 1397       title="Flags"
2959 27 Nov 06 nicklas 1398       description="Quality Flags: SNR1,SNR2 = low signal quality in color channel Cy5, Cy3; GS = low geometric score; MB = manually flagged bad."
2959 27 Nov 06 nicklas 1399       column="flags"
2959 27 Nov 06 nicklas 1400       type="string"
4027 30 Nov 07 enell 1401       averagemethod="none"
2959 27 Nov 06 nicklas 1402     />
2959 27 Nov 06 nicklas 1403     <property
2959 27 Nov 06 nicklas 1404       name="GS_Flags"
2959 27 Nov 06 nicklas 1405       title="GS flags"
2959 27 Nov 06 nicklas 1406       description="P = pass or M = marginal flag."
2959 27 Nov 06 nicklas 1407       column="gs_flags"
2959 27 Nov 06 nicklas 1408       type="string"
4027 30 Nov 07 enell 1409       averagemethod="none"
2959 27 Nov 06 nicklas 1410     />
2959 27 Nov 06 nicklas 1411     <property
2959 27 Nov 06 nicklas 1412       name="Cy3_Volume"
2959 27 Nov 06 nicklas 1413       title="Cy3 volume"
2959 27 Nov 06 nicklas 1414       description="Total integrated signal intensity in color channel Cy3."
2959 27 Nov 06 nicklas 1415       column="cy3_volume"
2959 27 Nov 06 nicklas 1416       channel="1"
2959 27 Nov 06 nicklas 1417       type="int"
4027 30 Nov 07 enell 1418       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1419     />
2959 27 Nov 06 nicklas 1420     <property
2959 27 Nov 06 nicklas 1421       name="Cy3_AvVolpixel"
2959 27 Nov 06 nicklas 1422       title="Cy3 average intensity"
2959 27 Nov 06 nicklas 1423       description="Average intensity per pixel in color channel Cy3."
2959 27 Nov 06 nicklas 1424       column="cy3_avg"
2959 27 Nov 06 nicklas 1425       channel="1"
2959 27 Nov 06 nicklas 1426       type="float"
4027 30 Nov 07 enell 1427       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1428     />
2959 27 Nov 06 nicklas 1429     <property
2959 27 Nov 06 nicklas 1430       name="Cy3_BGArith"
2959 27 Nov 06 nicklas 1431       title="Cy3 background (arithmetic)"
2959 27 Nov 06 nicklas 1432       description="Arithmetic average for local background in color channel Cy3."
2959 27 Nov 06 nicklas 1433       column="cy3_bg_arith"
2959 27 Nov 06 nicklas 1434       channel="1"
2959 27 Nov 06 nicklas 1435       type="float"
4027 30 Nov 07 enell 1436       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1437     />
2959 27 Nov 06 nicklas 1438     <property
2959 27 Nov 06 nicklas 1439       name="Cy3_BGGeom"
2959 27 Nov 06 nicklas 1440       title="Cy3 background (geometric)"
2959 27 Nov 06 nicklas 1441       description="Geometric average for local background in color channel Cy3."
2959 27 Nov 06 nicklas 1442       column="cy3_bg_geom"
2959 27 Nov 06 nicklas 1443       channel="1"
2959 27 Nov 06 nicklas 1444       type="float"
4027 30 Nov 07 enell 1445       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 1446     />
2959 27 Nov 06 nicklas 1447     <property
2959 27 Nov 06 nicklas 1448       name="Cy3_BGMedian"
2959 27 Nov 06 nicklas 1449       title="Cy3 background (median)"
2959 27 Nov 06 nicklas 1450       description="Median average for local background in color channel Cy3."
2959 27 Nov 06 nicklas 1451       column="cy3_bg_median"
2959 27 Nov 06 nicklas 1452       channel="1"
2959 27 Nov 06 nicklas 1453       type="float"
4027 30 Nov 07 enell 1454       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1455     />
2959 27 Nov 06 nicklas 1456     <property
2959 27 Nov 06 nicklas 1457       name="Cy3_BG_Tot"
2959 27 Nov 06 nicklas 1458       title="Cy3 background (total)"
2959 27 Nov 06 nicklas 1459       description="Total integrated background in color channel Cy3."
2959 27 Nov 06 nicklas 1460       column="cy3_bg_total"
2959 27 Nov 06 nicklas 1461       channel="1"
2959 27 Nov 06 nicklas 1462       type="float"
4027 30 Nov 07 enell 1463       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1464     />
2959 27 Nov 06 nicklas 1465     <property
2959 27 Nov 06 nicklas 1466       name="Cy3_VolBG"
2959 27 Nov 06 nicklas 1467       title="Cy3 reduced intensity"
2959 27 Nov 06 nicklas 1468       description="Background reduced intensity of colour channel Cy3."
2959 27 Nov 06 nicklas 1469       column="cy3_reduced"
2959 27 Nov 06 nicklas 1470       channel="1"
2959 27 Nov 06 nicklas 1471       type="float"
4027 30 Nov 07 enell 1472       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1473     />
2959 27 Nov 06 nicklas 1474     <property
2959 27 Nov 06 nicklas 1475       name="Cy3_Spotarea"
2959 27 Nov 06 nicklas 1476       title="Cy3 spot area"
2959 27 Nov 06 nicklas 1477       description="Area of spot in colour channel Cy3 in pixels."
2959 27 Nov 06 nicklas 1478       column="cy3_area"
2959 27 Nov 06 nicklas 1479       channel="1"
2959 27 Nov 06 nicklas 1480       type="float"
4027 30 Nov 07 enell 1481       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1482     />
2959 27 Nov 06 nicklas 1483     <property
2959 27 Nov 06 nicklas 1484       name="Cy3_Satpixel"
2959 27 Nov 06 nicklas 1485       title="Cy3 saturated pixels"
2959 27 Nov 06 nicklas 1486       description="Number of saturated pixel in color channel Cy3."
2959 27 Nov 06 nicklas 1487       column="cy3_saturated"
2959 27 Nov 06 nicklas 1488       channel="1"
2959 27 Nov 06 nicklas 1489       type="float"
4027 30 Nov 07 enell 1490       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1491     />
2959 27 Nov 06 nicklas 1492     <property
2959 27 Nov 06 nicklas 1493       name="Cy5_Volume"
2959 27 Nov 06 nicklas 1494       title="Cy5 volume"
2959 27 Nov 06 nicklas 1495       description="Total integrated signal intensity in color channel Cy5."
2959 27 Nov 06 nicklas 1496       column="cy5_volume"
2959 27 Nov 06 nicklas 1497       channel="2"
2959 27 Nov 06 nicklas 1498       type="int"
4027 30 Nov 07 enell 1499       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1500     />
2959 27 Nov 06 nicklas 1501     <property
2959 27 Nov 06 nicklas 1502       name="Cy5_AvVolpixel"
2959 27 Nov 06 nicklas 1503       title="Cy5 average intensity"
2959 27 Nov 06 nicklas 1504       description="Average intensity per pixel in color channel Cy5."
2959 27 Nov 06 nicklas 1505       column="cy5_avg"
2959 27 Nov 06 nicklas 1506       channel="2"
2959 27 Nov 06 nicklas 1507       type="float"
4027 30 Nov 07 enell 1508       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1509     />
2959 27 Nov 06 nicklas 1510     <property
2959 27 Nov 06 nicklas 1511       name="Cy5_BGArith"
2959 27 Nov 06 nicklas 1512       title="Cy5 background (arithmetic)"
2959 27 Nov 06 nicklas 1513       description="Arithmetic average for local background in color channel Cy5."
2959 27 Nov 06 nicklas 1514       column="cy5_bg_arith"
2959 27 Nov 06 nicklas 1515       channel="2"
2959 27 Nov 06 nicklas 1516       type="float"
4027 30 Nov 07 enell 1517       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1518     />
2959 27 Nov 06 nicklas 1519     <property
2959 27 Nov 06 nicklas 1520       name="Cy5_BGGeom"
2959 27 Nov 06 nicklas 1521       title="Cy5 background (geometric)"
2959 27 Nov 06 nicklas 1522       description="Geometric average for local background in color channel Cy5."
2959 27 Nov 06 nicklas 1523       column="cy5_bg_geom"
2959 27 Nov 06 nicklas 1524       channel="2"
2959 27 Nov 06 nicklas 1525       type="float"
4027 30 Nov 07 enell 1526       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 1527     />
2959 27 Nov 06 nicklas 1528     <property
2959 27 Nov 06 nicklas 1529       name="Cy5_BGMedian"
2959 27 Nov 06 nicklas 1530       title="Cy5 background (median)"
2959 27 Nov 06 nicklas 1531       description="Median average for local background in color channel Cy5."
2959 27 Nov 06 nicklas 1532       column="cy5_bg_median"
2959 27 Nov 06 nicklas 1533       channel="2"
2959 27 Nov 06 nicklas 1534       type="float"
4027 30 Nov 07 enell 1535       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1536     />
2959 27 Nov 06 nicklas 1537     <property
2959 27 Nov 06 nicklas 1538       name="Cy5_BG_Tot"
2959 27 Nov 06 nicklas 1539       title="Cy5 background (total)"
2959 27 Nov 06 nicklas 1540       description="Total integrated background in color channel Cy5."
2959 27 Nov 06 nicklas 1541       column="cy5_bg_total"
2959 27 Nov 06 nicklas 1542       channel="2"
2959 27 Nov 06 nicklas 1543       type="float"
4027 30 Nov 07 enell 1544       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1545     />
2959 27 Nov 06 nicklas 1546     <property
2959 27 Nov 06 nicklas 1547       name="Cy5_VolBG"
2959 27 Nov 06 nicklas 1548       title="Cy5 reduced intensity"
2959 27 Nov 06 nicklas 1549       description="Background reduced intensity of colour channel Cy5."
2959 27 Nov 06 nicklas 1550       column="cy5_reduced"
2959 27 Nov 06 nicklas 1551       channel="2"
2959 27 Nov 06 nicklas 1552       type="float"
4027 30 Nov 07 enell 1553       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1554     />
2959 27 Nov 06 nicklas 1555     <property
2959 27 Nov 06 nicklas 1556       name="Cy5_Spotarea"
2959 27 Nov 06 nicklas 1557       title="Cy5 spot area"
2959 27 Nov 06 nicklas 1558       description="Area of spot in colour channel Cy5 in pixels."
2959 27 Nov 06 nicklas 1559       column="cy5_area"
2959 27 Nov 06 nicklas 1560       channel="2"
2959 27 Nov 06 nicklas 1561       type="float"
4027 30 Nov 07 enell 1562       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1563     />
2959 27 Nov 06 nicklas 1564     <property
2959 27 Nov 06 nicklas 1565       name="Cy5_Satpixel"
2959 27 Nov 06 nicklas 1566       title="Cy5 saturated pixels"
2959 27 Nov 06 nicklas 1567       description="Number of saturated pixel in color channel Cy5."
2959 27 Nov 06 nicklas 1568       column="cy5_saturated"
2959 27 Nov 06 nicklas 1569       channel="2"
2959 27 Nov 06 nicklas 1570       type="float"
4027 30 Nov 07 enell 1571       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1572     />
2959 27 Nov 06 nicklas 1573     <property
2959 27 Nov 06 nicklas 1574       name="Rep_vol_BG2"
2959 27 Nov 06 nicklas 1575       title="Background reduced volume"
2959 27 Nov 06 nicklas 1576       description="Average of background reduced volume for onchip replicas (when calculated)."
2959 27 Nov 06 nicklas 1577       column="rep_vol"
2959 27 Nov 06 nicklas 1578       type="float"
4027 30 Nov 07 enell 1579       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1580     />
2959 27 Nov 06 nicklas 1581     <property
2959 27 Nov 06 nicklas 1582       name="RatioCy5Cy3"
2959 27 Nov 06 nicklas 1583       title="Direct ratio"
2959 27 Nov 06 nicklas 1584       description="Direct ratio ( = Cy5_Vol-BG / Cy3_Vol-BG )."
2959 27 Nov 06 nicklas 1585       column="ratio"
2959 27 Nov 06 nicklas 1586       type="float"
4027 30 Nov 07 enell 1587       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 1588     />
2959 27 Nov 06 nicklas 1589     <property
2959 27 Nov 06 nicklas 1590       name="Directional_RatioCy5Cy3"
2959 27 Nov 06 nicklas 1591       title="Directional ratio"
2959 27 Nov 06 nicklas 1592       description="Directional ratio: if Ratio &gt; 1 then Directional = Ratio, if Ratio &gt; 1 then Directional = -1/Ratio."
2959 27 Nov 06 nicklas 1593       column="directional_ratio"
2959 27 Nov 06 nicklas 1594       type="float"
4027 30 Nov 07 enell 1595       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 1596     />
2959 27 Nov 06 nicklas 1597     <property
2959 27 Nov 06 nicklas 1598       name="Log2_RatioCy5Cy3"
2959 27 Nov 06 nicklas 1599       title="Log2 ratio"
2959 27 Nov 06 nicklas 1600       description="Log2 ratio: log2 (Ratio-Cy5/Cy3)"
2959 27 Nov 06 nicklas 1601       column="log2_ratio"
2959 27 Nov 06 nicklas 1602       type="float"
4027 30 Nov 07 enell 1603       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1604     />
2959 27 Nov 06 nicklas 1605     <property
2959 27 Nov 06 nicklas 1606       name="Comp_ChannelCy3"
2959 27 Nov 06 nicklas 1607       title="Cy53 normalised intensity"
2959 27 Nov 06 nicklas 1608       description="Normalised intensity of Cy3_Vol-BG."
2959 27 Nov 06 nicklas 1609       column="cy3_normalised"
2959 27 Nov 06 nicklas 1610       channel="1"
2959 27 Nov 06 nicklas 1611       type="float"
4027 30 Nov 07 enell 1612       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1613     />
2959 27 Nov 06 nicklas 1614     <property
2959 27 Nov 06 nicklas 1615       name="Comp_ChannelCy5"
2959 27 Nov 06 nicklas 1616       title="Cy5 normalised intensity"
2959 27 Nov 06 nicklas 1617       description="Normalised intensity of Cy5_Vol-BG."
2959 27 Nov 06 nicklas 1618       column="cy5_normalised"
2959 27 Nov 06 nicklas 1619       channel="2"
2959 27 Nov 06 nicklas 1620       type="float"
4027 30 Nov 07 enell 1621       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1622     />
2959 27 Nov 06 nicklas 1623     <property
2959 27 Nov 06 nicklas 1624       name="Comp_RatioCy5Cy3"
2959 27 Nov 06 nicklas 1625       title="Compensated ratio"
2959 27 Nov 06 nicklas 1626       description="Compensated ratio ( = Comp_Channel Cy5 / Comp_Channel Cy3 )."
2959 27 Nov 06 nicklas 1627       column="compensated_ratio"
2959 27 Nov 06 nicklas 1628       type="float"
4027 30 Nov 07 enell 1629       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 1630     />
2959 27 Nov 06 nicklas 1631     <property
2959 27 Nov 06 nicklas 1632       name="Comp_Directional_RatioCy5Cy3"
2959 27 Nov 06 nicklas 1633       title="Compensated directional ratio"
2959 27 Nov 06 nicklas 1634       description="Compensated directional ratio: if Comp_Ratio &gt; 1 then Directional = Ratio, if Ratio &lt; 1 then Directional = -1/Ratio."
2959 27 Nov 06 nicklas 1635       column="comp_dir_ratio"
2959 27 Nov 06 nicklas 1636       type="float"
4027 30 Nov 07 enell 1637       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 1638     />
2959 27 Nov 06 nicklas 1639     <property
2959 27 Nov 06 nicklas 1640       name="Comp_Log2_Ratio"
2959 27 Nov 06 nicklas 1641       title="Compensated log2 ratio"
2959 27 Nov 06 nicklas 1642       description="Compensated Log2 ratio: log2 (Comp_Ratio-Cy5/Cy3)."
2959 27 Nov 06 nicklas 1643       column="comp_log2_ratio"
2959 27 Nov 06 nicklas 1644       type="float"
4027 30 Nov 07 enell 1645       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1646     />
2959 27 Nov 06 nicklas 1647     <property
2959 27 Nov 06 nicklas 1648       name="Comment"
2959 27 Nov 06 nicklas 1649       title="Comment"
2959 27 Nov 06 nicklas 1650       description="Additional description of spot."
2959 27 Nov 06 nicklas 1651       column="comment"
2959 27 Nov 06 nicklas 1652       type="string"
4027 30 Nov 07 enell 1653       averagemethod="none"
2959 27 Nov 06 nicklas 1654     />
2959 27 Nov 06 nicklas 1655     <property
2959 27 Nov 06 nicklas 1656       name="SNRtot"
2959 27 Nov 06 nicklas 1657       title="Squared average SNR"
2959 27 Nov 06 nicklas 1658       description="Squared average of Cy5_SNR and Cy3_SNR."
2959 27 Nov 06 nicklas 1659       column="snr_tot"
2959 27 Nov 06 nicklas 1660       type="float"
4027 30 Nov 07 enell 1661       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 1662     />
2959 27 Nov 06 nicklas 1663     <property
2959 27 Nov 06 nicklas 1664       name="SNRtot_Score"
2959 27 Nov 06 nicklas 1665       title="Squared average score SNR"
2959 27 Nov 06 nicklas 1666       description="Squared average of Cy5_%SNR and Cy3_%SNR."
2959 27 Nov 06 nicklas 1667       column="snr_tot_score"
2959 27 Nov 06 nicklas 1668       type="float"
4027 30 Nov 07 enell 1669       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 1670     />
2959 27 Nov 06 nicklas 1671     <property
2959 27 Nov 06 nicklas 1672       name="SNRGS"
2959 27 Nov 06 nicklas 1673       title="Saturated pixel"
2959 27 Nov 06 nicklas 1674       description="Number of saturated pixel in both colors (logical or)."
2959 27 Nov 06 nicklas 1675       column="sat_pixels"
2959 27 Nov 06 nicklas 1676       type="float"
4027 30 Nov 07 enell 1677       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1678     />
2959 27 Nov 06 nicklas 1679     <property
2959 27 Nov 06 nicklas 1680       name="Replicas"
2959 27 Nov 06 nicklas 1681       title="Replicas"
2959 27 Nov 06 nicklas 1682       description="Replicas"
2959 27 Nov 06 nicklas 1683       column="replicas"
2959 27 Nov 06 nicklas 1684       type="float"
4027 30 Nov 07 enell 1685       averagemethod="none"
2959 27 Nov 06 nicklas 1686     />
2959 27 Nov 06 nicklas 1687     <property
2959 27 Nov 06 nicklas 1688       name="Regulation"
2959 27 Nov 06 nicklas 1689       title="Regulation"
2959 27 Nov 06 nicklas 1690       description="If Flag = SNR1 then Regulation=&gt;Down; if Flag = SNR2 then Regulation=&gt;up; if Flag = SNR1 AND SNR2 then Regulation=>&gt;weak; else Regulation = Ratio-Cy5/Cy3."
2959 27 Nov 06 nicklas 1691       column="regulation"
2959 27 Nov 06 nicklas 1692       type="string"
4027 30 Nov 07 enell 1693       averagemethod="none"
2959 27 Nov 06 nicklas 1694     />
2959 27 Nov 06 nicklas 1695     <property
2959 27 Nov 06 nicklas 1696       name="GroupName"
2959 27 Nov 06 nicklas 1697       title="Group name"
2959 27 Nov 06 nicklas 1698       description="Group name for this spot."
2959 27 Nov 06 nicklas 1699       column="group_name"
2959 27 Nov 06 nicklas 1700       type="string"
4027 30 Nov 07 enell 1701       averagemethod="none"
2959 27 Nov 06 nicklas 1702     />
2959 27 Nov 06 nicklas 1703     <property
2959 27 Nov 06 nicklas 1704       name="MedianRatios"
2959 27 Nov 06 nicklas 1705       title="Median of ratios"
2959 27 Nov 06 nicklas 1706       description="Median of ratios (Cy5/Cy3) from all pixel in this spot."
2959 27 Nov 06 nicklas 1707       column="median_ratios"
2959 27 Nov 06 nicklas 1708       type="float"
4027 30 Nov 07 enell 1709       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 1710     />
2959 27 Nov 06 nicklas 1711     <property
2959 27 Nov 06 nicklas 1712       name="MedianRatiosSDev"
2959 27 Nov 06 nicklas 1713       title="Median of ratios (sdev%)"
2959 27 Nov 06 nicklas 1714       description="Standard deviation of Median of ratios in percent."
2959 27 Nov 06 nicklas 1715       column="median_ratios_sdev"
2959 27 Nov 06 nicklas 1716       type="float"
4027 30 Nov 07 enell 1717       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1718     />
2959 27 Nov 06 nicklas 1719     <property
2959 27 Nov 06 nicklas 1720       name="RatioMedians"
2959 27 Nov 06 nicklas 1721       title="Ratio of medians"
2959 27 Nov 06 nicklas 1722       description="Ratio of Medians (Cy5/Cy3) from all pixel in this spot."
2959 27 Nov 06 nicklas 1723       column="ratio_medians"
2959 27 Nov 06 nicklas 1724       type="float"
4027 30 Nov 07 enell 1725       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 1726     />
2959 27 Nov 06 nicklas 1727     <property
2959 27 Nov 06 nicklas 1728       name="RatioMediansSDev"
2959 27 Nov 06 nicklas 1729       title="Ratio of medians (sdev%)"
2959 27 Nov 06 nicklas 1730       description="Standard deviation of Ratio of medians in percent."
2959 27 Nov 06 nicklas 1731       column="ratio_medians_sdev"
2959 27 Nov 06 nicklas 1732       type="float"
4027 30 Nov 07 enell 1733       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1734     />
2959 27 Nov 06 nicklas 1735     <intensity-formula
2959 27 Nov 06 nicklas 1736       name="Volume"
2959 27 Nov 06 nicklas 1737       title="Volume"
2959 27 Nov 06 nicklas 1738       description="Total integrated signal intensity"
2959 27 Nov 06 nicklas 1739       >
2959 27 Nov 06 nicklas 1740       <formula 
2959 27 Nov 06 nicklas 1741         channel="1"
2959 27 Nov 06 nicklas 1742         expression="raw('Cy3_Volume')"
2959 27 Nov 06 nicklas 1743       />
2959 27 Nov 06 nicklas 1744       <formula 
2959 27 Nov 06 nicklas 1745         channel="2"
2959 27 Nov 06 nicklas 1746         expression="raw('Cy5_Volume')"
2959 27 Nov 06 nicklas 1747       />
2959 27 Nov 06 nicklas 1748     </intensity-formula>
2959 27 Nov 06 nicklas 1749     <intensity-formula
2959 27 Nov 06 nicklas 1750       name="VolBG"
2959 27 Nov 06 nicklas 1751       title="Reduced intensity"
2959 27 Nov 06 nicklas 1752       description="Background reduced intensity"
2959 27 Nov 06 nicklas 1753       >
2959 27 Nov 06 nicklas 1754       <formula 
2959 27 Nov 06 nicklas 1755         channel="1"
2959 27 Nov 06 nicklas 1756         expression="raw('Cy3_VolBG')"
2959 27 Nov 06 nicklas 1757       />
2959 27 Nov 06 nicklas 1758       <formula 
2959 27 Nov 06 nicklas 1759         channel="2"
2959 27 Nov 06 nicklas 1760         expression="raw('Cy5_VolBG')"
2959 27 Nov 06 nicklas 1761       />
2959 27 Nov 06 nicklas 1762     </intensity-formula>
2959 27 Nov 06 nicklas 1763   </raw-data-type>
2959 27 Nov 06 nicklas 1764
2959 27 Nov 06 nicklas 1765   <raw-data-type
2959 27 Nov 06 nicklas 1766     id="genetac"
2959 27 Nov 06 nicklas 1767     channels="2"
2959 27 Nov 06 nicklas 1768     name="GeneTAC"
2959 27 Nov 06 nicklas 1769     table="RawDataGeneTac"
2959 27 Nov 06 nicklas 1770     >
2959 27 Nov 06 nicklas 1771     <property
2959 27 Nov 06 nicklas 1772       name="medCy3"
2959 27 Nov 06 nicklas 1773       title="Signal median Cy3"
2959 27 Nov 06 nicklas 1774       description="Median of Cy3 signal intensity."
2959 27 Nov 06 nicklas 1775       column="med_cy3"
2959 27 Nov 06 nicklas 1776       channel="1"
2959 27 Nov 06 nicklas 1777       type="float"
4027 30 Nov 07 enell 1778       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1779     />
2959 27 Nov 06 nicklas 1780     <property
2959 27 Nov 06 nicklas 1781       name="medCy5"
2959 27 Nov 06 nicklas 1782       title="Signal median Cy5"
2959 27 Nov 06 nicklas 1783       description="Median of Cy5 signal intensity."
2959 27 Nov 06 nicklas 1784       column="med_cy5"
2959 27 Nov 06 nicklas 1785       channel="2"
2959 27 Nov 06 nicklas 1786       type="float"
4027 30 Nov 07 enell 1787       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1788     />
2959 27 Nov 06 nicklas 1789     <property
2959 27 Nov 06 nicklas 1790       name="medRatio"
2959 27 Nov 06 nicklas 1791       title="Signal median ratio"
2959 27 Nov 06 nicklas 1792       description="Ratio of median signal."
2959 27 Nov 06 nicklas 1793       column="med_ratio"
2959 27 Nov 06 nicklas 1794       type="float"
4027 30 Nov 07 enell 1795       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 1796     />
2959 27 Nov 06 nicklas 1797     <property
2959 27 Nov 06 nicklas 1798       name="bgCy3"
2959 27 Nov 06 nicklas 1799       title="Background median Cy3"
2959 27 Nov 06 nicklas 1800       description="Median of background intensity for Cy3."
2959 27 Nov 06 nicklas 1801       column="bg_cy3"
2959 27 Nov 06 nicklas 1802       channel="1"
2959 27 Nov 06 nicklas 1803       type="float"
4027 30 Nov 07 enell 1804       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1805     />
2959 27 Nov 06 nicklas 1806     <property
2959 27 Nov 06 nicklas 1807       name="bgCy5"
2959 27 Nov 06 nicklas 1808       title="Background median Cy5"
2959 27 Nov 06 nicklas 1809       description="Median of background intensity for Cy5."
2959 27 Nov 06 nicklas 1810       column="bg_cy5"
2959 27 Nov 06 nicklas 1811       channel="2"
2959 27 Nov 06 nicklas 1812       type="float"
4027 30 Nov 07 enell 1813       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1814     />
2959 27 Nov 06 nicklas 1815     <property
2959 27 Nov 06 nicklas 1816       name="bgRatio"
2959 27 Nov 06 nicklas 1817       title="Signal med ratio"
2959 27 Nov 06 nicklas 1818       description="Ratio of median background."
2959 27 Nov 06 nicklas 1819       column="bg_ratio"
2959 27 Nov 06 nicklas 1820       type="float"
4027 30 Nov 07 enell 1821       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 1822     />
2959 27 Nov 06 nicklas 1823     <intensity-formula
2959 27 Nov 06 nicklas 1824       name="medianfg"
2959 27 Nov 06 nicklas 1825       title="Median FG"
2959 27 Nov 06 nicklas 1826       description="Median foreground"
2959 27 Nov 06 nicklas 1827       >
2959 27 Nov 06 nicklas 1828       <formula 
2959 27 Nov 06 nicklas 1829         channel="1"
2959 27 Nov 06 nicklas 1830         expression="raw('medCy3')"
2959 27 Nov 06 nicklas 1831       />
2959 27 Nov 06 nicklas 1832       <formula 
2959 27 Nov 06 nicklas 1833         channel="2"
2959 27 Nov 06 nicklas 1834         expression="raw('medCy5')"
2959 27 Nov 06 nicklas 1835       />
2959 27 Nov 06 nicklas 1836     </intensity-formula>
2959 27 Nov 06 nicklas 1837     <intensity-formula
2959 27 Nov 06 nicklas 1838       name="median"
2959 27 Nov 06 nicklas 1839       title="Median FG - Median BG"
2959 27 Nov 06 nicklas 1840       description="Subtract median background from median foreground"
2959 27 Nov 06 nicklas 1841       >
2959 27 Nov 06 nicklas 1842       <formula 
2959 27 Nov 06 nicklas 1843         channel="1"
2959 27 Nov 06 nicklas 1844         expression="raw('medCy3') - raw('bgCy3')"
2959 27 Nov 06 nicklas 1845       />
2959 27 Nov 06 nicklas 1846       <formula 
2959 27 Nov 06 nicklas 1847         channel="2"
2959 27 Nov 06 nicklas 1848         expression="raw('medCy5') - raw('bgCy5')"
2959 27 Nov 06 nicklas 1849       />
2959 27 Nov 06 nicklas 1850     </intensity-formula>
2959 27 Nov 06 nicklas 1851   </raw-data-type>
2959 27 Nov 06 nicklas 1852   
2959 27 Nov 06 nicklas 1853   <raw-data-type
2959 27 Nov 06 nicklas 1854     id="imagene"
2959 27 Nov 06 nicklas 1855     channels="2"
2959 27 Nov 06 nicklas 1856     name="ImaGene"
2959 27 Nov 06 nicklas 1857     table="RawDataImaGene"
2959 27 Nov 06 nicklas 1858     >
2959 27 Nov 06 nicklas 1859     <property
2959 27 Nov 06 nicklas 1860       name="Field"
2959 27 Nov 06 nicklas 1861       title="Field"
2959 27 Nov 06 nicklas 1862       description="Name of a field where the spot is located."
2959 27 Nov 06 nicklas 1863       column="field"
2959 27 Nov 06 nicklas 1864       type="string"
4027 30 Nov 07 enell 1865       averagemethod="none"
2959 27 Nov 06 nicklas 1866     />
2959 27 Nov 06 nicklas 1867     <property
2959 27 Nov 06 nicklas 1868       name="Flag_Cy3"
2959 27 Nov 06 nicklas 1869       title="Flag cy3"
2959 27 Nov 06 nicklas 1870       description="Numeric code for the spot (0 - no flag, flag codes 1,...,7)."
2959 27 Nov 06 nicklas 1871       column="cy3_flag"
2959 27 Nov 06 nicklas 1872       channel="1"
2959 27 Nov 06 nicklas 1873       type="int"
4027 30 Nov 07 enell 1874       averagemethod="none"
2959 27 Nov 06 nicklas 1875     />
2959 27 Nov 06 nicklas 1876     <property
2959 27 Nov 06 nicklas 1877       name="SignalMean_Cy3"
2959 27 Nov 06 nicklas 1878       title="Mean signal cy3"
2959 27 Nov 06 nicklas 1879       description="Pixel intensity averaged over the local signal region."
2959 27 Nov 06 nicklas 1880       column="cy3_mean_signal"
2959 27 Nov 06 nicklas 1881       channel="1"
2959 27 Nov 06 nicklas 1882       type="float"
2959 27 Nov 06 nicklas 1883     />
2959 27 Nov 06 nicklas 1884     <property
2959 27 Nov 06 nicklas 1885       name="BackgroundMean_Cy3"
2959 27 Nov 06 nicklas 1886       title="Mean background cy3"
2959 27 Nov 06 nicklas 1887       description="Pixel intensity averaged over the local background region."
2959 27 Nov 06 nicklas 1888       column="cy3_mean_bg"
2959 27 Nov 06 nicklas 1889       channel="1"
2959 27 Nov 06 nicklas 1890       type="float"
4027 30 Nov 07 enell 1891       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1892     />
2959 27 Nov 06 nicklas 1893     <property
2959 27 Nov 06 nicklas 1894       name="SignalMedian_Cy3"
2959 27 Nov 06 nicklas 1895       title="Median signal cy3"
2959 27 Nov 06 nicklas 1896       description="Median pixel intensity computed over the local signal region."
2959 27 Nov 06 nicklas 1897       column="cy3_median_signal"
2959 27 Nov 06 nicklas 1898       channel="1"
2959 27 Nov 06 nicklas 1899       type="float"
4027 30 Nov 07 enell 1900       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1901     />
2959 27 Nov 06 nicklas 1902     <property
2959 27 Nov 06 nicklas 1903       name="BackgroundMedian_Cy3"
2959 27 Nov 06 nicklas 1904       title="Median background cy3"
2959 27 Nov 06 nicklas 1905       description="Median pixel intensity averaged over the local background region."
2959 27 Nov 06 nicklas 1906       column="cy3_median_bg"
2959 27 Nov 06 nicklas 1907       channel="1"
2959 27 Nov 06 nicklas 1908       type="float"
4027 30 Nov 07 enell 1909       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1910     />
2959 27 Nov 06 nicklas 1911     <property
2959 27 Nov 06 nicklas 1912       name="SignalMode_Cy3"
2959 27 Nov 06 nicklas 1913       title="Mode signal cy3"
2959 27 Nov 06 nicklas 1914       description="Mode pixel intensity computed over the local signal region (mode corresponds to the peak location in intensity distribution)."
2959 27 Nov 06 nicklas 1915       column="cy3_mode_signal"
2959 27 Nov 06 nicklas 1916       channel="1"
2959 27 Nov 06 nicklas 1917       type="float"
4027 30 Nov 07 enell 1918       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1919     />
2959 27 Nov 06 nicklas 1920     <property
2959 27 Nov 06 nicklas 1921       name="BackgroundMode_Cy3"
2959 27 Nov 06 nicklas 1922       title="Mode background cy3"
2959 27 Nov 06 nicklas 1923       description="Mode pixel intensity computed over the local background region."
2959 27 Nov 06 nicklas 1924       column="cy3_mode_bg"
2959 27 Nov 06 nicklas 1925       channel="1"
2959 27 Nov 06 nicklas 1926       type="float"
4027 30 Nov 07 enell 1927       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1928     />
2959 27 Nov 06 nicklas 1929     <property
2959 27 Nov 06 nicklas 1930       name="SignalArea_Cy3"
2959 27 Nov 06 nicklas 1931       title="Signal area cy3"
2959 27 Nov 06 nicklas 1932       description="Number of pixels in the local signal region."
2959 27 Nov 06 nicklas 1933       column="cy3_area_signal"
2959 27 Nov 06 nicklas 1934       channel="1"
2959 27 Nov 06 nicklas 1935       type="int"
4027 30 Nov 07 enell 1936       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1937     />
2959 27 Nov 06 nicklas 1938     <property
2959 27 Nov 06 nicklas 1939       name="BackgroundArea_Cy3"
2959 27 Nov 06 nicklas 1940       title="Background area cy3"
2959 27 Nov 06 nicklas 1941       description="Number of pixels in the local background region."
2959 27 Nov 06 nicklas 1942       column="cy3_area_bg"
2959 27 Nov 06 nicklas 1943       channel="1"
2959 27 Nov 06 nicklas 1944       type="int"
4027 30 Nov 07 enell 1945       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1946     />
2959 27 Nov 06 nicklas 1947     <property
2959 27 Nov 06 nicklas 1948       name="SignalTotal_Cy3"
2959 27 Nov 06 nicklas 1949       title="Total signal cy3"
2959 27 Nov 06 nicklas 1950       description="Total pixel intensity summed over the local signal region."
2959 27 Nov 06 nicklas 1951       column="cy3_total_signal"
2959 27 Nov 06 nicklas 1952       channel="1"
2959 27 Nov 06 nicklas 1953       type="int"
4027 30 Nov 07 enell 1954       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1955     />
2959 27 Nov 06 nicklas 1956     <property
2959 27 Nov 06 nicklas 1957       name="BackgroundTotal_Cy3"
2959 27 Nov 06 nicklas 1958       title="Total background cy3"
2959 27 Nov 06 nicklas 1959       description="Total pixel intensity summed over the local background region."
2959 27 Nov 06 nicklas 1960       column="cy3_total_bg"
2959 27 Nov 06 nicklas 1961       channel="1"
2959 27 Nov 06 nicklas 1962       type="int"
4027 30 Nov 07 enell 1963       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1964     />
2959 27 Nov 06 nicklas 1965     <property
2959 27 Nov 06 nicklas 1966       name="ShapeRegularity_Cy3"
2959 27 Nov 06 nicklas 1967       title="Shape regularity cy3"
2959 27 Nov 06 nicklas 1968       description="The signal area of a spot is inscribed into a circle, then the number of non-signal pixels that fall within this circle is computed and divided by area of circle. This ratio is subtracted from 1 to give the Shape Regularity."
2959 27 Nov 06 nicklas 1969       column="cy3_shape"
2959 27 Nov 06 nicklas 1970       channel="1"
2959 27 Nov 06 nicklas 1971       type="float"
4027 30 Nov 07 enell 1972       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 1973     />
2959 27 Nov 06 nicklas 1974     <property
2959 27 Nov 06 nicklas 1975       name="IgnoredArea_Cy3"
2959 27 Nov 06 nicklas 1976       title="Ignored area cy3"
2959 27 Nov 06 nicklas 1977       description="Area of ignored regions directly neighboring (touching) the signal area is computed."
2959 27 Nov 06 nicklas 1978       column="cy3_area_ignored"
2959 27 Nov 06 nicklas 1979       channel="1"
2959 27 Nov 06 nicklas 1980       type="int"
4027 30 Nov 07 enell 1981       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1982     />
2959 27 Nov 06 nicklas 1983     <property
2959 27 Nov 06 nicklas 1984       name="SpotArea_Cy3"
2959 27 Nov 06 nicklas 1985       title="Spot area cy3"
2959 27 Nov 06 nicklas 1986       description="Signal Area plus Ignored Area."
2959 27 Nov 06 nicklas 1987       column="cy3_area_spot"
2959 27 Nov 06 nicklas 1988       channel="1"
2959 27 Nov 06 nicklas 1989       type="int"
4027 30 Nov 07 enell 1990       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 1991     />
2959 27 Nov 06 nicklas 1992     <property
2959 27 Nov 06 nicklas 1993       name="IgnoredMedian_Cy3"
2959 27 Nov 06 nicklas 1994       title="Median ignored cy3"
2959 27 Nov 06 nicklas 1995       description="Median pixel intensity computed over the local ignored region."
2959 27 Nov 06 nicklas 1996       column="cy3_median_ignored"
2959 27 Nov 06 nicklas 1997       channel="1"
2959 27 Nov 06 nicklas 1998       type="float"
4027 30 Nov 07 enell 1999       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2000     />
2959 27 Nov 06 nicklas 2001     <property
2959 27 Nov 06 nicklas 2002       name="AreaToPerimeter_Cy3"
2959 27 Nov 06 nicklas 2003       title="Area to perimeter cy3"
2959 27 Nov 06 nicklas 2004       description="This quality measure defines the spot's circularity. Area of a spot is divided by a square of spot perimeter and multiplied by 4&#960;. As a result, this measure ranges from 0 (highly non-circular shape) to 1 (a perfect circle)."
2959 27 Nov 06 nicklas 2005       column="cy3_area_perimeter"
2959 27 Nov 06 nicklas 2006       channel="1"
2959 27 Nov 06 nicklas 2007       type="float"
4027 30 Nov 07 enell 2008       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2009     />
2959 27 Nov 06 nicklas 2010     <property
2959 27 Nov 06 nicklas 2011       name="OpenPerimeter_Cy3"
2959 27 Nov 06 nicklas 2012       title="Open perimeter cy3"
2959 27 Nov 06 nicklas 2013       description="Computes the proportion of signal perimeter that touches the border of rectangular snip around the spot."
2959 27 Nov 06 nicklas 2014       column="cy3_open_perimeter"
2959 27 Nov 06 nicklas 2015       channel="1"
2959 27 Nov 06 nicklas 2016       type="float"
4027 30 Nov 07 enell 2017       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2018     />
2959 27 Nov 06 nicklas 2019     <property
2959 27 Nov 06 nicklas 2020       name="XCoord_Cy3"
2959 27 Nov 06 nicklas 2021       title="X coordinate cy3"
2959 27 Nov 06 nicklas 2022       description="X coordinate (in pixels) of grid circle corresponding to the spot."
2959 27 Nov 06 nicklas 2023       column="cy3_x"
2959 27 Nov 06 nicklas 2024       channel="1"
2959 27 Nov 06 nicklas 2025       type="float"
4027 30 Nov 07 enell 2026       averagemethod="none"
2959 27 Nov 06 nicklas 2027     />
2959 27 Nov 06 nicklas 2028     <property
2959 27 Nov 06 nicklas 2029       name="YCoord_Cy3"
2959 27 Nov 06 nicklas 2030       title="Y coordinate cy3"
2959 27 Nov 06 nicklas 2031       description="Y coordinate (in pixels) of grid circle corresponding to the spot."
2959 27 Nov 06 nicklas 2032       column="cy3_y"
2959 27 Nov 06 nicklas 2033       channel="1"
2959 27 Nov 06 nicklas 2034       type="float"
4027 30 Nov 07 enell 2035       averagemethod="none"
2959 27 Nov 06 nicklas 2036     />
2959 27 Nov 06 nicklas 2037     <property
2959 27 Nov 06 nicklas 2038       name="Diameter_Cy3"
2959 27 Nov 06 nicklas 2039       title="Diameter cy3"
2959 27 Nov 06 nicklas 2040       description="Diameter (in pixels) of grid circle corresponding to the spot."
2959 27 Nov 06 nicklas 2041       column="cy3_diameter"
2959 27 Nov 06 nicklas 2042       channel="1"
2959 27 Nov 06 nicklas 2043       type="int"
4027 30 Nov 07 enell 2044       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2045     />
2959 27 Nov 06 nicklas 2046     <property
2959 27 Nov 06 nicklas 2047       name="PositionOffset_Cy3"
2959 27 Nov 06 nicklas 2048       title="Position offset cy3"
2959 27 Nov 06 nicklas 2049       description="Offset (in pixels) of the center of the grid circle from the expected position in the grid."
2959 27 Nov 06 nicklas 2050       column="cy3_offset"
2959 27 Nov 06 nicklas 2051       channel="1"
2959 27 Nov 06 nicklas 2052       type="float"
4027 30 Nov 07 enell 2053       averagemethod="none"
2959 27 Nov 06 nicklas 2054     />
2959 27 Nov 06 nicklas 2055     <property
2959 27 Nov 06 nicklas 2056       name="OffsetX_Cy3"
2959 27 Nov 06 nicklas 2057       title="X offset cy3"
2959 27 Nov 06 nicklas 2058       description="X Offset (in pixels) of the center of the grid circle from the expected position in the grid."
2959 27 Nov 06 nicklas 2059       column="cy3_offset_x"
2959 27 Nov 06 nicklas 2060       channel="1"
2959 27 Nov 06 nicklas 2061       type="float"
4027 30 Nov 07 enell 2062       averagemethod="none"
2959 27 Nov 06 nicklas 2063     />
2959 27 Nov 06 nicklas 2064     <property
2959 27 Nov 06 nicklas 2065       name="OffsetY_Cy3"
2959 27 Nov 06 nicklas 2066       title="Y offset cy3"
2959 27 Nov 06 nicklas 2067       description="Y Offset (in pixels) of the center of the grid circle from the expected position in the grid."
2959 27 Nov 06 nicklas 2068       column="cy3_offset_y"
2959 27 Nov 06 nicklas 2069       channel="1"
2959 27 Nov 06 nicklas 2070       type="float"
4027 30 Nov 07 enell 2071       averagemethod="none"
2959 27 Nov 06 nicklas 2072     />
2959 27 Nov 06 nicklas 2073     <property
2959 27 Nov 06 nicklas 2074       name="ExpectedX_Cy3"
2959 27 Nov 06 nicklas 2075       title="X expected cy3"
2959 27 Nov 06 nicklas 2076       description="X coordinate of expected position of the circle in the grid. Expected position in the grid is computed fitting least square lines to circle centers in every row and column."
2959 27 Nov 06 nicklas 2077       column="cy3_x_expected"
2959 27 Nov 06 nicklas 2078       channel="1"
2959 27 Nov 06 nicklas 2079       type="float"
4027 30 Nov 07 enell 2080       averagemethod="none"
2959 27 Nov 06 nicklas 2081     />
2959 27 Nov 06 nicklas 2082     <property
2959 27 Nov 06 nicklas 2083       name="ExpectedY_Cy3"
2959 27 Nov 06 nicklas 2084       title="Y expected cy3"
2959 27 Nov 06 nicklas 2085       description="Y coordinate of expected position of the circle in the grid. Expected position in the grid is computed fitting least square lines to circle centers in every row and column."
2959 27 Nov 06 nicklas 2086       column="cy3_y_expected"
2959 27 Nov 06 nicklas 2087       channel="1"
2959 27 Nov 06 nicklas 2088       type="float"
4027 30 Nov 07 enell 2089       averagemethod="none"
2959 27 Nov 06 nicklas 2090     />
2959 27 Nov 06 nicklas 2091     <property
2959 27 Nov 06 nicklas 2092       name="CMX_Cy3"
2959 27 Nov 06 nicklas 2093       title="CM X coordinate cy3"
2959 27 Nov 06 nicklas 2094       description="X coordinate of the center of the mass of spot's signal region."
2959 27 Nov 06 nicklas 2095       column="cy3_x_cm"
2959 27 Nov 06 nicklas 2096       channel="1"
2959 27 Nov 06 nicklas 2097       type="float"
4027 30 Nov 07 enell 2098       averagemethod="none"
2959 27 Nov 06 nicklas 2099     />
2959 27 Nov 06 nicklas 2100     <property
2959 27 Nov 06 nicklas 2101       name="CMY_Cy3"
2959 27 Nov 06 nicklas 2102       title="CM Y coordinate cy3"
2959 27 Nov 06 nicklas 2103       description="Y coordinate of the center of the mass of spot's signal region."
2959 27 Nov 06 nicklas 2104       column="cy3_y_cm"
2959 27 Nov 06 nicklas 2105       channel="1"
2959 27 Nov 06 nicklas 2106       type="float"
4027 30 Nov 07 enell 2107       averagemethod="none"
2959 27 Nov 06 nicklas 2108     />
2959 27 Nov 06 nicklas 2109     <property
2959 27 Nov 06 nicklas 2110       name="CMOffset_Cy3"
2959 27 Nov 06 nicklas 2111       title="CM offset cy3"
2959 27 Nov 06 nicklas 2112       description="Offset (in pixels) of the spot's center of the mass from the expected position in the grid."
2959 27 Nov 06 nicklas 2113       column="cy3_offset_cm"
2959 27 Nov 06 nicklas 2114       channel="1"
2959 27 Nov 06 nicklas 2115       type="float"
4027 30 Nov 07 enell 2116       averagemethod="none"
2959 27 Nov 06 nicklas 2117     />
2959 27 Nov 06 nicklas 2118     <property
2959 27 Nov 06 nicklas 2119       name="CMOffsetX_Cy3"
2959 27 Nov 06 nicklas 2120       title="CM X offset cy3"
2959 27 Nov 06 nicklas 2121       description="X offset (in pixels) of the spot's center of the mass from the expected position in the grid."
2959 27 Nov 06 nicklas 2122       column="cy3_offset_x_cm"
2959 27 Nov 06 nicklas 2123       channel="1"
2959 27 Nov 06 nicklas 2124       type="float"
4027 30 Nov 07 enell 2125       averagemethod="none"
2959 27 Nov 06 nicklas 2126     />
2959 27 Nov 06 nicklas 2127     <property
2959 27 Nov 06 nicklas 2128       name="CMOffsetY_Cy3"
2959 27 Nov 06 nicklas 2129       title="CM Y offset cy3"
2959 27 Nov 06 nicklas 2130       description="Y offset (in pixels) of the spot's center of the mass from the expected position in the grid."
2959 27 Nov 06 nicklas 2131       column="cy3_offset_y_cm"
2959 27 Nov 06 nicklas 2132       channel="1"
2959 27 Nov 06 nicklas 2133       type="float"
4027 30 Nov 07 enell 2134       averagemethod="none"
2959 27 Nov 06 nicklas 2135     />
2959 27 Nov 06 nicklas 2136     <property
2959 27 Nov 06 nicklas 2137       name="MinDiam_Cy3"
2959 27 Nov 06 nicklas 2138       title="Min diameter cy3"
2959 27 Nov 06 nicklas 2139       description="Diameter of the circle inscribed into the spot's signal region."
2959 27 Nov 06 nicklas 2140       column="cy3_diameter_min"
2959 27 Nov 06 nicklas 2141       channel="1"
2959 27 Nov 06 nicklas 2142       type="float"
4027 30 Nov 07 enell 2143       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2144     />
2959 27 Nov 06 nicklas 2145     <property
2959 27 Nov 06 nicklas 2146       name="MaxDiam_Cy3"
2959 27 Nov 06 nicklas 2147       title="Max diameter cy3"
2959 27 Nov 06 nicklas 2148       description="Diameter of the circle, the spot's signal region can be inscribed in."
2959 27 Nov 06 nicklas 2149       column="cy3_diameter_max"
2959 27 Nov 06 nicklas 2150       channel="1"
2959 27 Nov 06 nicklas 2151       type="float"
4027 30 Nov 07 enell 2152       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2153     />
2959 27 Nov 06 nicklas 2154     <property
2959 27 Nov 06 nicklas 2155       name="Control_Cy3"
2959 27 Nov 06 nicklas 2156       title="Control cy3"
2959 27 Nov 06 nicklas 2157       description="Name of a control type for current spot (no name means the spot is not a control spot)."
2959 27 Nov 06 nicklas 2158       column="cy3_control"
2959 27 Nov 06 nicklas 2159       channel="1"
2959 27 Nov 06 nicklas 2160       type="string"
4027 30 Nov 07 enell 2161       averagemethod="none"
2959 27 Nov 06 nicklas 2162     />
2959 27 Nov 06 nicklas 2163     <property
2959 27 Nov 06 nicklas 2164       name="FailedControl_Cy3"
2959 27 Nov 06 nicklas 2165       title="Failed control cy3"
2959 27 Nov 06 nicklas 2166       description="0 if the control passed all tests, 1 if at least one of the tests failed."
2959 27 Nov 06 nicklas 2167       column="cy3_control_failed"
2959 27 Nov 06 nicklas 2168       channel="1"
2959 27 Nov 06 nicklas 2169       type="boolean"
4027 30 Nov 07 enell 2170       averagemethod="none"
2959 27 Nov 06 nicklas 2171     />
2959 27 Nov 06 nicklas 2172     <property
2959 27 Nov 06 nicklas 2173       name="BackgroundContaminationPresent_Cy3"
2959 27 Nov 06 nicklas 2174       title="Bg contamination cy3"
2959 27 Nov 06 nicklas 2175       description="0 if the spot passed background contamination test, 1 if it did not."
2959 27 Nov 06 nicklas 2176       column="cy3_bg_contamination"
2959 27 Nov 06 nicklas 2177       channel="1"
2959 27 Nov 06 nicklas 2178       type="boolean"
4027 30 Nov 07 enell 2179       averagemethod="none"
2959 27 Nov 06 nicklas 2180     />
2959 27 Nov 06 nicklas 2181     <property
2959 27 Nov 06 nicklas 2182       name="SignalContaminationPresent_Cy3"
2959 27 Nov 06 nicklas 2183       title="Signal contamination cy3"
2959 27 Nov 06 nicklas 2184       description="0 if the spot passed signal contamination test, 1 if it did not."
2959 27 Nov 06 nicklas 2185       column="cy3_signal_contamination"
2959 27 Nov 06 nicklas 2186       channel="1"
2959 27 Nov 06 nicklas 2187       type="boolean"
4027 30 Nov 07 enell 2188       averagemethod="none"
2959 27 Nov 06 nicklas 2189     />
2959 27 Nov 06 nicklas 2190     <property
2959 27 Nov 06 nicklas 2191       name="IgnoredFailed_Cy3"
2959 27 Nov 06 nicklas 2192       title="Ignored % failed cy3"
2959 27 Nov 06 nicklas 2193       description="0 if the spot passed ignored percentage test, 1 if it did not."
2959 27 Nov 06 nicklas 2194       column="cy3_ignored_failed"
2959 27 Nov 06 nicklas 2195       channel="1"
2959 27 Nov 06 nicklas 2196       type="boolean"
4027 30 Nov 07 enell 2197       averagemethod="none"
2959 27 Nov 06 nicklas 2198     />
2959 27 Nov 06 nicklas 2199     <property
2959 27 Nov 06 nicklas 2200       name="OpenPerimeterFailed_Cy3"
2959 27 Nov 06 nicklas 2201       title="Open perimeter failed cy3"
2959 27 Nov 06 nicklas 2202       description="0 if the spot passed open perimeter test, 1 if it did not."
2959 27 Nov 06 nicklas 2203       column="cy3_perimeter_failed"
2959 27 Nov 06 nicklas 2204       channel="1"
2959 27 Nov 06 nicklas 2205       type="boolean"
4027 30 Nov 07 enell 2206       averagemethod="none"
2959 27 Nov 06 nicklas 2207     />
2959 27 Nov 06 nicklas 2208     <property
2959 27 Nov 06 nicklas 2209       name="ShapeRegularityFailed_Cy3"
2959 27 Nov 06 nicklas 2210       title="Shape regularity failed cy3"
2959 27 Nov 06 nicklas 2211       description="0 if the spot passed shape regularity test, 1 if it did not."
2959 27 Nov 06 nicklas 2212       column="cy3_shape_failed"
2959 27 Nov 06 nicklas 2213       channel="1"
2959 27 Nov 06 nicklas 2214       type="boolean"
4027 30 Nov 07 enell 2215       averagemethod="none"
2959 27 Nov 06 nicklas 2216     />
2959 27 Nov 06 nicklas 2217     <property
2959 27 Nov 06 nicklas 2218       name="PerimToAreaFailed_Cy3"
2959 27 Nov 06 nicklas 2219       title="Perimeter to area failed cy3"
2959 27 Nov 06 nicklas 2220       description="0 if the spot passed perimeter-to-area test, 1 if it did not."
2959 27 Nov 06 nicklas 2221       column="cy3_areapm_failed"
2959 27 Nov 06 nicklas 2222       channel="1"
2959 27 Nov 06 nicklas 2223       type="boolean"
4027 30 Nov 07 enell 2224       averagemethod="none"
2959 27 Nov 06 nicklas 2225     />
2959 27 Nov 06 nicklas 2226     <property
2959 27 Nov 06 nicklas 2227       name="OffsetFailed_Cy3"
2959 27 Nov 06 nicklas 2228       title="Offset failed cy3"
2959 27 Nov 06 nicklas 2229       description="0 if the spot passed offset test, 1 if it did not."
2959 27 Nov 06 nicklas 2230       column="cy3_offset_failed"
2959 27 Nov 06 nicklas 2231       channel="1"
2959 27 Nov 06 nicklas 2232       type="boolean"
4027 30 Nov 07 enell 2233       averagemethod="none"
2959 27 Nov 06 nicklas 2234     />
2959 27 Nov 06 nicklas 2235     <property
2959 27 Nov 06 nicklas 2236       name="EmptySpot_Cy3"
2959 27 Nov 06 nicklas 2237       title="Empty spot cy3"
2959 27 Nov 06 nicklas 2238       description="1 if the spot is empty, 0 if not."
2959 27 Nov 06 nicklas 2239       column="cy3_empty_spot"
2959 27 Nov 06 nicklas 2240       channel="1"
2959 27 Nov 06 nicklas 2241       type="boolean"
4027 30 Nov 07 enell 2242       averagemethod="none"
2959 27 Nov 06 nicklas 2243     />
2959 27 Nov 06 nicklas 2244     <property
2959 27 Nov 06 nicklas 2245       name="NegativeSpot_Cy3"
2959 27 Nov 06 nicklas 2246       title="Negative spot cy3"
2959 27 Nov 06 nicklas 2247       description="1 if the spot was qualified as negative, 0 if it was not."
2959 27 Nov 06 nicklas 2248       column="cy3_negative_spot"
2959 27 Nov 06 nicklas 2249       channel="1"
2959 27 Nov 06 nicklas 2250       type="boolean"
4027 30 Nov 07 enell 2251       averagemethod="none"
2959 27 Nov 06 nicklas 2252     />
2959 27 Nov 06 nicklas 2253     <property
2959 27 Nov 06 nicklas 2254       name="SelectedSpot_Cy3"
2959 27 Nov 06 nicklas 2255       title="Selected spot cy3"
2959 27 Nov 06 nicklas 2256       description="1 if the spot was selected in the software view at time of save, 0 if not."
2959 27 Nov 06 nicklas 2257       column="cy3_selected_spot"
2959 27 Nov 06 nicklas 2258       channel="1"
2959 27 Nov 06 nicklas 2259       type="boolean"
4027 30 Nov 07 enell 2260       averagemethod="none"
2959 27 Nov 06 nicklas 2261     />
2959 27 Nov 06 nicklas 2262     <property
2959 27 Nov 06 nicklas 2263       name="SaturatedSpot_Cy3"
2959 27 Nov 06 nicklas 2264       title="Saturated spot cy3"
2959 27 Nov 06 nicklas 2265       description="1 if the spot was qualified as saturated, 0 if it was not."
2959 27 Nov 06 nicklas 2266       column="cy3_saturated_spot"
2959 27 Nov 06 nicklas 2267       channel="1"
2959 27 Nov 06 nicklas 2268       type="boolean"
4027 30 Nov 07 enell 2269       averagemethod="none"
2959 27 Nov 06 nicklas 2270     />
2959 27 Nov 06 nicklas 2271     <property
2959 27 Nov 06 nicklas 2272       name="SignalMean_Cy5"
2959 27 Nov 06 nicklas 2273       title="Mean signal cy5"
2959 27 Nov 06 nicklas 2274       description="Pixel intensity averaged over the local signal region."
2959 27 Nov 06 nicklas 2275       column="cy5_mean_signal"
2959 27 Nov 06 nicklas 2276       channel="2"
2959 27 Nov 06 nicklas 2277       type="float"
4027 30 Nov 07 enell 2278       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2279     />
2959 27 Nov 06 nicklas 2280     <property
2959 27 Nov 06 nicklas 2281       name="BackgroundMean_Cy5"
2959 27 Nov 06 nicklas 2282       title="Mean background cy5"
2959 27 Nov 06 nicklas 2283       description="Pixel intensity averaged over the local background region."
2959 27 Nov 06 nicklas 2284       column="cy5_mean_bg"
2959 27 Nov 06 nicklas 2285       channel="2"
2959 27 Nov 06 nicklas 2286       type="float"
4027 30 Nov 07 enell 2287       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2288     />
2959 27 Nov 06 nicklas 2289     <property
2959 27 Nov 06 nicklas 2290       name="SignalMedian_Cy5"
2959 27 Nov 06 nicklas 2291       title="Median signal cy5"
2959 27 Nov 06 nicklas 2292       description="Median pixel intensity computed over the local signal region."
2959 27 Nov 06 nicklas 2293       column="cy5_median_signal"
2959 27 Nov 06 nicklas 2294       channel="2"
2959 27 Nov 06 nicklas 2295       type="float"
4027 30 Nov 07 enell 2296       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2297     />
2959 27 Nov 06 nicklas 2298     <property
2959 27 Nov 06 nicklas 2299       name="BackgroundMedian_Cy5"
2959 27 Nov 06 nicklas 2300       title="Median background cy5"
2959 27 Nov 06 nicklas 2301       description="Median pixel intensity averaged over the local background region."
2959 27 Nov 06 nicklas 2302       column="cy5_median_bg"
2959 27 Nov 06 nicklas 2303       channel="2"
2959 27 Nov 06 nicklas 2304       type="float"
4027 30 Nov 07 enell 2305       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2306     />
2959 27 Nov 06 nicklas 2307     <property
2959 27 Nov 06 nicklas 2308       name="SignalMode_Cy5"
2959 27 Nov 06 nicklas 2309       title="Mode signal cy5"
2959 27 Nov 06 nicklas 2310       description="Mode pixel intensity computed over the local signal region (mode corresponds to the peak location in intensity distribution)."
2959 27 Nov 06 nicklas 2311       column="cy5_mode_signal"
2959 27 Nov 06 nicklas 2312       channel="2"
2959 27 Nov 06 nicklas 2313       type="float"
4027 30 Nov 07 enell 2314       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2315     />
2959 27 Nov 06 nicklas 2316     <property
2959 27 Nov 06 nicklas 2317       name="BackgroundMode_Cy5"
2959 27 Nov 06 nicklas 2318       title="Mode background cy5"
2959 27 Nov 06 nicklas 2319       description="Mode pixel intensity computed over the local background region."
2959 27 Nov 06 nicklas 2320       column="cy5_mode_bg"
2959 27 Nov 06 nicklas 2321       channel="2"
2959 27 Nov 06 nicklas 2322       type="float"
4027 30 Nov 07 enell 2323       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2324     />
2959 27 Nov 06 nicklas 2325     <property
2959 27 Nov 06 nicklas 2326       name="SignalArea_Cy5"
2959 27 Nov 06 nicklas 2327       title="Signal area cy5"
2959 27 Nov 06 nicklas 2328       description="Number of pixels in the local signal region."
2959 27 Nov 06 nicklas 2329       column="cy5_area_signal"
2959 27 Nov 06 nicklas 2330       channel="2"
2959 27 Nov 06 nicklas 2331       type="int"
4027 30 Nov 07 enell 2332       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2333     />
2959 27 Nov 06 nicklas 2334     <property
2959 27 Nov 06 nicklas 2335       name="BackgroundArea_Cy5"
2959 27 Nov 06 nicklas 2336       title="Background area cy5"
2959 27 Nov 06 nicklas 2337       description="Number of pixels in the local background region."
2959 27 Nov 06 nicklas 2338       column="cy5_area_bg"
2959 27 Nov 06 nicklas 2339       channel="2"
2959 27 Nov 06 nicklas 2340       type="int"
4027 30 Nov 07 enell 2341       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2342     />
2959 27 Nov 06 nicklas 2343     <property
2959 27 Nov 06 nicklas 2344       name="SignalTotal_Cy5"
2959 27 Nov 06 nicklas 2345       title="Total signal cy5"
2959 27 Nov 06 nicklas 2346       description="Total pixel intensity summed over the local signal region."
2959 27 Nov 06 nicklas 2347       column="cy5_total_signal"
2959 27 Nov 06 nicklas 2348       channel="2"
2959 27 Nov 06 nicklas 2349       type="int"
4027 30 Nov 07 enell 2350       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2351     />
2959 27 Nov 06 nicklas 2352     <property
2959 27 Nov 06 nicklas 2353       name="BackgroundTotal_Cy5"
2959 27 Nov 06 nicklas 2354       title="Total background cy5"
2959 27 Nov 06 nicklas 2355       description="Total pixel intensity summed over the local background region."
2959 27 Nov 06 nicklas 2356       column="cy5_total_bg"
2959 27 Nov 06 nicklas 2357       channel="2"
2959 27 Nov 06 nicklas 2358       type="int"
4027 30 Nov 07 enell 2359       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2360     />
2959 27 Nov 06 nicklas 2361     <property
2959 27 Nov 06 nicklas 2362       name="ShapeRegularity_Cy5"
2959 27 Nov 06 nicklas 2363       title="Shape regularity cy5"
2959 27 Nov 06 nicklas 2364       description="The signal area of a spot is inscribed into a circle, then the number of non-signal pixels that fall within this circle is computed and divided by area of circle. This ratio is subtracted from 1 to give the Shape Regularity."
2959 27 Nov 06 nicklas 2365       column="cy5_shape"
2959 27 Nov 06 nicklas 2366       channel="2"
2959 27 Nov 06 nicklas 2367       type="float"
4027 30 Nov 07 enell 2368       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2369     />
2959 27 Nov 06 nicklas 2370     <property
2959 27 Nov 06 nicklas 2371       name="IgnoredArea_Cy5"
2959 27 Nov 06 nicklas 2372       title="Ignored area cy5"
2959 27 Nov 06 nicklas 2373       description="Area of ignored regions directly neighboring (touching) the signal area is computed."
2959 27 Nov 06 nicklas 2374       column="cy5_area_ignored"
2959 27 Nov 06 nicklas 2375       channel="2"
2959 27 Nov 06 nicklas 2376       type="int"
4027 30 Nov 07 enell 2377       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2378     />
2959 27 Nov 06 nicklas 2379     <property
2959 27 Nov 06 nicklas 2380       name="SpotArea_Cy5"
2959 27 Nov 06 nicklas 2381       title="Spot area cy5"
2959 27 Nov 06 nicklas 2382       description="Signal Area plus Ignored Area."
2959 27 Nov 06 nicklas 2383       column="cy5_area_spot"
2959 27 Nov 06 nicklas 2384       channel="2"
2959 27 Nov 06 nicklas 2385       type="int"
4027 30 Nov 07 enell 2386       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2387     />
2959 27 Nov 06 nicklas 2388     <property
2959 27 Nov 06 nicklas 2389       name="IgnoredMedian_Cy5"
2959 27 Nov 06 nicklas 2390       title="Median ignored cy5"
2959 27 Nov 06 nicklas 2391       description="Median pixel intensity computed over the local ignored region."
2959 27 Nov 06 nicklas 2392       column="cy5_median_ignored"
2959 27 Nov 06 nicklas 2393       channel="2"
2959 27 Nov 06 nicklas 2394       type="float"
4027 30 Nov 07 enell 2395       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2396     />
2959 27 Nov 06 nicklas 2397     <property
2959 27 Nov 06 nicklas 2398       name="AreaToPerimeter_Cy5"
2959 27 Nov 06 nicklas 2399       title="Area to perimeter cy5"
2959 27 Nov 06 nicklas 2400       description="This quality measure defines the spot's circularity. Area of a spot is divided by a square of spot perimeter and multiplied by 4&#960;. As a result, this measure ranges from 0 (highly non-circular shape) to 1 (a perfect circle)."
2959 27 Nov 06 nicklas 2401       column="cy5_area_perimeter"
2959 27 Nov 06 nicklas 2402       channel="2"
2959 27 Nov 06 nicklas 2403       type="float"
4027 30 Nov 07 enell 2404       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2405     />
2959 27 Nov 06 nicklas 2406     <property
2959 27 Nov 06 nicklas 2407       name="OpenPerimeter_Cy5"
2959 27 Nov 06 nicklas 2408       title="Open perimeter cy5"
2959 27 Nov 06 nicklas 2409       description="Computes the proportion of signal perimeter that touches the border of rectangular snip around the spot."
2959 27 Nov 06 nicklas 2410       column="cy5_open_perimeter"
2959 27 Nov 06 nicklas 2411       channel="2"
2959 27 Nov 06 nicklas 2412       type="float"
4027 30 Nov 07 enell 2413       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2414     />
2959 27 Nov 06 nicklas 2415     <property
2959 27 Nov 06 nicklas 2416       name="XCoord_Cy5"
2959 27 Nov 06 nicklas 2417       title="X coordinate cy5"
2959 27 Nov 06 nicklas 2418       description="X coordinate (in pixels) of grid circle corresponding to the spot."
2959 27 Nov 06 nicklas 2419       column="cy5_x"
2959 27 Nov 06 nicklas 2420       channel="2"
2959 27 Nov 06 nicklas 2421       type="float"
4027 30 Nov 07 enell 2422       averagemethod="none"
2959 27 Nov 06 nicklas 2423     />
2959 27 Nov 06 nicklas 2424     <property
2959 27 Nov 06 nicklas 2425       name="YCoord_Cy5"
2959 27 Nov 06 nicklas 2426       title="Y coordinate cy5"
2959 27 Nov 06 nicklas 2427       description="Y coordinate (in pixels) of grid circle corresponding to the spot."
2959 27 Nov 06 nicklas 2428       column="cy5_y"
2959 27 Nov 06 nicklas 2429       channel="2"
2959 27 Nov 06 nicklas 2430       type="float"
4027 30 Nov 07 enell 2431       averagemethod="none"
2959 27 Nov 06 nicklas 2432     />
2959 27 Nov 06 nicklas 2433     <property
2959 27 Nov 06 nicklas 2434       name="Diameter_Cy5"
2959 27 Nov 06 nicklas 2435       title="Diameter cy5"
2959 27 Nov 06 nicklas 2436       description="Diameter (in pixels) of grid circle corresponding to the spot."
2959 27 Nov 06 nicklas 2437       column="cy5_diameter"
2959 27 Nov 06 nicklas 2438       channel="2"
2959 27 Nov 06 nicklas 2439       type="int"
4027 30 Nov 07 enell 2440       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2441     />
2959 27 Nov 06 nicklas 2442     <property
2959 27 Nov 06 nicklas 2443       name="PositionOffset_Cy5"
2959 27 Nov 06 nicklas 2444       title="Position offset cy5"
2959 27 Nov 06 nicklas 2445       description="Offset (in pixels) of the center of the grid circle from the expected position in the grid."
2959 27 Nov 06 nicklas 2446       column="cy5_offset"
2959 27 Nov 06 nicklas 2447       channel="2"
2959 27 Nov 06 nicklas 2448       type="float"
4027 30 Nov 07 enell 2449       averagemethod="none"
2959 27 Nov 06 nicklas 2450     />
2959 27 Nov 06 nicklas 2451     <property
2959 27 Nov 06 nicklas 2452       name="OffsetX_Cy5"
2959 27 Nov 06 nicklas 2453       title="X offset cy5"
2959 27 Nov 06 nicklas 2454       description="X Offset (in pixels) of the center of the grid circle from the expected position in the grid."
2959 27 Nov 06 nicklas 2455       column="cy5_offset_x"
2959 27 Nov 06 nicklas 2456       channel="2"
2959 27 Nov 06 nicklas 2457       type="float"
4027 30 Nov 07 enell 2458       averagemethod="none"
2959 27 Nov 06 nicklas 2459     />
2959 27 Nov 06 nicklas 2460     <property
2959 27 Nov 06 nicklas 2461       name="OffsetY_Cy5"
2959 27 Nov 06 nicklas 2462       title="Y offset cy5"
2959 27 Nov 06 nicklas 2463       description="Y Offset (in pixels) of the center of the grid circle from the expected position in the grid."
2959 27 Nov 06 nicklas 2464       column="cy5_offset_y"
2959 27 Nov 06 nicklas 2465       channel="2"
2959 27 Nov 06 nicklas 2466       type="float"
4027 30 Nov 07 enell 2467       averagemethod="none"
2959 27 Nov 06 nicklas 2468     />
2959 27 Nov 06 nicklas 2469     <property
2959 27 Nov 06 nicklas 2470       name="ExpectedX_Cy5"
2959 27 Nov 06 nicklas 2471       title="X expected cy5"
2959 27 Nov 06 nicklas 2472       description="X coordinate of expected position of the circle in the grid. Expected position in the grid is computed fitting least square lines to circle centers in every row and column."
2959 27 Nov 06 nicklas 2473       column="cy5_x_expected"
2959 27 Nov 06 nicklas 2474       channel="2"
2959 27 Nov 06 nicklas 2475       type="float"
4027 30 Nov 07 enell 2476       averagemethod="none"
2959 27 Nov 06 nicklas 2477     />
2959 27 Nov 06 nicklas 2478     <property
2959 27 Nov 06 nicklas 2479       name="ExpectedY_Cy5"
2959 27 Nov 06 nicklas 2480       title="Y expected cy5"
2959 27 Nov 06 nicklas 2481       description="Y coordinate of expected position of the circle in the grid. Expected position in the grid is computed fitting least square lines to circle centers in every row and column."
2959 27 Nov 06 nicklas 2482       column="cy5_y_expected"
2959 27 Nov 06 nicklas 2483       channel="2"
2959 27 Nov 06 nicklas 2484       type="float"
4027 30 Nov 07 enell 2485       averagemethod="none"
2959 27 Nov 06 nicklas 2486     />
2959 27 Nov 06 nicklas 2487     <property
2959 27 Nov 06 nicklas 2488       name="CMX_Cy5"
2959 27 Nov 06 nicklas 2489       title="CM X coordinate cy5"
2959 27 Nov 06 nicklas 2490       description="X coordinate of the center of the mass of spot's signal region."
2959 27 Nov 06 nicklas 2491       column="cy5_x_cm"
2959 27 Nov 06 nicklas 2492       channel="2"
2959 27 Nov 06 nicklas 2493       type="float"
4027 30 Nov 07 enell 2494       averagemethod="none"
2959 27 Nov 06 nicklas 2495     />
2959 27 Nov 06 nicklas 2496     <property
2959 27 Nov 06 nicklas 2497       name="CMY_Cy5"
2959 27 Nov 06 nicklas 2498       title="CM Y coordinate cy5"
2959 27 Nov 06 nicklas 2499       description="Y coordinate of the center of the mass of spot's signal region."
2959 27 Nov 06 nicklas 2500       column="cy5_y_cm"
2959 27 Nov 06 nicklas 2501       channel="2"
2959 27 Nov 06 nicklas 2502       type="float"
4027 30 Nov 07 enell 2503       averagemethod="none"
2959 27 Nov 06 nicklas 2504     />
2959 27 Nov 06 nicklas 2505     <property
2959 27 Nov 06 nicklas 2506       name="CMOffset_Cy5"
2959 27 Nov 06 nicklas 2507       title="CM offset cy5"
2959 27 Nov 06 nicklas 2508       description="Offset (in pixels) of the spot's center of the mass from the expected position in the grid."
2959 27 Nov 06 nicklas 2509       column="cy5_offset_cm"
2959 27 Nov 06 nicklas 2510       channel="2"
2959 27 Nov 06 nicklas 2511       type="float"
4027 30 Nov 07 enell 2512       averagemethod="none"
2959 27 Nov 06 nicklas 2513     />
2959 27 Nov 06 nicklas 2514     <property
2959 27 Nov 06 nicklas 2515       name="CMOffsetX_Cy5"
2959 27 Nov 06 nicklas 2516       title="CM X offset cy5"
2959 27 Nov 06 nicklas 2517       description="X offset (in pixels) of the spot's center of the mass from the expected position in the grid."
2959 27 Nov 06 nicklas 2518       column="cy5_offset_x_cm"
2959 27 Nov 06 nicklas 2519       channel="2"
2959 27 Nov 06 nicklas 2520       type="float"
4027 30 Nov 07 enell 2521       averagemethod="none"
2959 27 Nov 06 nicklas 2522     />
2959 27 Nov 06 nicklas 2523     <property
2959 27 Nov 06 nicklas 2524       name="CMOffsetY_Cy5"
2959 27 Nov 06 nicklas 2525       title="CM Y offset cy5"
2959 27 Nov 06 nicklas 2526       description="Y offset (in pixels) of the spot's center of the mass from the expected position in the grid."
2959 27 Nov 06 nicklas 2527       column="cy5_offset_y_cm"
2959 27 Nov 06 nicklas 2528       channel="2"
2959 27 Nov 06 nicklas 2529       type="float"
4027 30 Nov 07 enell 2530       averagemethod="none"
2959 27 Nov 06 nicklas 2531     />
2959 27 Nov 06 nicklas 2532     <property
2959 27 Nov 06 nicklas 2533       name="MinDiam_Cy5"
2959 27 Nov 06 nicklas 2534       title="Min diameter cy5"
2959 27 Nov 06 nicklas 2535       description="Diameter of the circle inscribed into the spot's signal region."
2959 27 Nov 06 nicklas 2536       column="cy5_diameter_min"
2959 27 Nov 06 nicklas 2537       channel="2"
2959 27 Nov 06 nicklas 2538       type="float"
4027 30 Nov 07 enell 2539       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2540     />
2959 27 Nov 06 nicklas 2541     <property
2959 27 Nov 06 nicklas 2542       name="MaxDiam_Cy5"
2959 27 Nov 06 nicklas 2543       title="Max diameter cy5"
2959 27 Nov 06 nicklas 2544       description="Diameter of the circle, the spot's signal region can be inscribed in."
2959 27 Nov 06 nicklas 2545       column="cy5_diameter_max"
2959 27 Nov 06 nicklas 2546       channel="2"
2959 27 Nov 06 nicklas 2547       type="float"
4027 30 Nov 07 enell 2548       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2549     />
2959 27 Nov 06 nicklas 2550     <property
2959 27 Nov 06 nicklas 2551       name="Control_Cy5"
2959 27 Nov 06 nicklas 2552       title="Control cy5"
2959 27 Nov 06 nicklas 2553       description="Name of a control type for current spot (no name means the spot is not a control spot)."
2959 27 Nov 06 nicklas 2554       column="cy5_control"
2959 27 Nov 06 nicklas 2555       channel="2"
2959 27 Nov 06 nicklas 2556       type="string"
4027 30 Nov 07 enell 2557       averagemethod="none"
2959 27 Nov 06 nicklas 2558     />
2959 27 Nov 06 nicklas 2559     <property
2959 27 Nov 06 nicklas 2560       name="FailedControl_Cy5"
2959 27 Nov 06 nicklas 2561       title="Failed control cy5"
2959 27 Nov 06 nicklas 2562       description="0 if the control passed all tests, 1 if at least one of the tests failed."
2959 27 Nov 06 nicklas 2563       column="cy5_control_failed"
2959 27 Nov 06 nicklas 2564       channel="2"
2959 27 Nov 06 nicklas 2565       type="boolean"
4027 30 Nov 07 enell 2566       averagemethod="none"
2959 27 Nov 06 nicklas 2567     />
2959 27 Nov 06 nicklas 2568     <property
2959 27 Nov 06 nicklas 2569       name="BackgroundContaminationPresent_Cy5"
2959 27 Nov 06 nicklas 2570       title="Bg contamination cy5"
2959 27 Nov 06 nicklas 2571       description="0 if the spot passed background contamination test, 1 if it did not."
2959 27 Nov 06 nicklas 2572       column="cy5_bg_contamination"
2959 27 Nov 06 nicklas 2573       channel="2"
2959 27 Nov 06 nicklas 2574       type="boolean"
4027 30 Nov 07 enell 2575       averagemethod="none"
2959 27 Nov 06 nicklas 2576     />
2959 27 Nov 06 nicklas 2577     <property
2959 27 Nov 06 nicklas 2578       name="SignalContaminationPresent_Cy5"
2959 27 Nov 06 nicklas 2579       title="Signal contamination cy5"
2959 27 Nov 06 nicklas 2580       description="0 if the spot passed signal contamination test, 1 if it did not."
2959 27 Nov 06 nicklas 2581       column="cy5_signal_contamination"
2959 27 Nov 06 nicklas 2582       channel="2"
2959 27 Nov 06 nicklas 2583       type="boolean"
4027 30 Nov 07 enell 2584       averagemethod="none"
2959 27 Nov 06 nicklas 2585     />
2959 27 Nov 06 nicklas 2586     <property
2959 27 Nov 06 nicklas 2587       name="IgnoredFailed_Cy5"
2959 27 Nov 06 nicklas 2588       title="Ignored % failed cy5"
2959 27 Nov 06 nicklas 2589       description="0 if the spot passed ignored percentage test, 1 if it did not."
2959 27 Nov 06 nicklas 2590       column="cy5_ignored_failed"
2959 27 Nov 06 nicklas 2591       channel="2"
2959 27 Nov 06 nicklas 2592       type="boolean"
4027 30 Nov 07 enell 2593       averagemethod="none"
2959 27 Nov 06 nicklas 2594     />
2959 27 Nov 06 nicklas 2595     <property
2959 27 Nov 06 nicklas 2596       name="OpenPerimeterFailed_Cy5"
2959 27 Nov 06 nicklas 2597       title="Open perimeter failed cy5"
2959 27 Nov 06 nicklas 2598       description="0 if the spot passed open perimeter test, 1 if it did not."
2959 27 Nov 06 nicklas 2599       column="cy5_perimeter_failed"
2959 27 Nov 06 nicklas 2600       channel="2"
2959 27 Nov 06 nicklas 2601       type="boolean"
4027 30 Nov 07 enell 2602       averagemethod="none"
2959 27 Nov 06 nicklas 2603     />
2959 27 Nov 06 nicklas 2604     <property
2959 27 Nov 06 nicklas 2605       name="ShapeRegularityFailed_Cy5"
2959 27 Nov 06 nicklas 2606       title="Shape regularity failed cy5"
2959 27 Nov 06 nicklas 2607       description="0 if the spot passed shape regularity test, 1 if it did not."
2959 27 Nov 06 nicklas 2608       column="cy5_shape_failed"
2959 27 Nov 06 nicklas 2609       channel="2"
2959 27 Nov 06 nicklas 2610       type="boolean"
4027 30 Nov 07 enell 2611       averagemethod="none"
2959 27 Nov 06 nicklas 2612     />
2959 27 Nov 06 nicklas 2613     <property
2959 27 Nov 06 nicklas 2614       name="PerimToAreaFailed_Cy5"
2959 27 Nov 06 nicklas 2615       title="Perimeter to area failed cy5"
2959 27 Nov 06 nicklas 2616       description="0 if the spot passed perimeter-to-area test, 1 if it did not."
2959 27 Nov 06 nicklas 2617       column="cy5_areapm_failed"
2959 27 Nov 06 nicklas 2618       channel="2"
2959 27 Nov 06 nicklas 2619       type="boolean"
4027 30 Nov 07 enell 2620       averagemethod="none"
2959 27 Nov 06 nicklas 2621     />
2959 27 Nov 06 nicklas 2622     <property
2959 27 Nov 06 nicklas 2623       name="OffsetFailed_Cy5"
2959 27 Nov 06 nicklas 2624       title="Offset failed cy5"
2959 27 Nov 06 nicklas 2625       description="0 if the spot passed offset test, 1 if it did not."
2959 27 Nov 06 nicklas 2626       column="cy5_offset_failed"
2959 27 Nov 06 nicklas 2627       channel="2"
2959 27 Nov 06 nicklas 2628       type="boolean"
4027 30 Nov 07 enell 2629       averagemethod="none"
2959 27 Nov 06 nicklas 2630     />
2959 27 Nov 06 nicklas 2631     <property
2959 27 Nov 06 nicklas 2632       name="EmptySpot_Cy5"
2959 27 Nov 06 nicklas 2633       title="Empty spot cy5"
2959 27 Nov 06 nicklas 2634       description="1 if the spot is empty, 0 if not."
2959 27 Nov 06 nicklas 2635       column="cy5_empty_spot"
2959 27 Nov 06 nicklas 2636       channel="2"
2959 27 Nov 06 nicklas 2637       type="boolean"
4027 30 Nov 07 enell 2638       averagemethod="none"
2959 27 Nov 06 nicklas 2639     />
2959 27 Nov 06 nicklas 2640     <property
2959 27 Nov 06 nicklas 2641       name="NegativeSpot_Cy5"
2959 27 Nov 06 nicklas 2642       title="Negative spot cy5"
2959 27 Nov 06 nicklas 2643       description="1 if the spot was qualified as negative, 0 if it was not."
2959 27 Nov 06 nicklas 2644       column="cy5_negative_spot"
2959 27 Nov 06 nicklas 2645       channel="2"
2959 27 Nov 06 nicklas 2646       type="boolean"
4027 30 Nov 07 enell 2647       averagemethod="none"
2959 27 Nov 06 nicklas 2648     />
2959 27 Nov 06 nicklas 2649     <property
2959 27 Nov 06 nicklas 2650       name="SelectedSpot_Cy5"
2959 27 Nov 06 nicklas 2651       title="Selected spot cy5"
2959 27 Nov 06 nicklas 2652       description="1 if the spot was selected in the software view at time of save, 0 if not."
2959 27 Nov 06 nicklas 2653       column="cy5_selected_spot"
2959 27 Nov 06 nicklas 2654       channel="2"
2959 27 Nov 06 nicklas 2655       type="boolean"
4027 30 Nov 07 enell 2656       averagemethod="none"
2959 27 Nov 06 nicklas 2657     />
2959 27 Nov 06 nicklas 2658     <property
2959 27 Nov 06 nicklas 2659       name="SaturatedSpot_Cy5"
2959 27 Nov 06 nicklas 2660       title="Saturated spot cy5"
2959 27 Nov 06 nicklas 2661       description="1 if the spot was qualified as saturated, 0 if it was not."
2959 27 Nov 06 nicklas 2662       column="cy5_saturated_spot"
2959 27 Nov 06 nicklas 2663       channel="2"
2959 27 Nov 06 nicklas 2664       type="boolean"
4027 30 Nov 07 enell 2665       averagemethod="none"
2959 27 Nov 06 nicklas 2666     />
2959 27 Nov 06 nicklas 2667     <intensity-formula
2959 27 Nov 06 nicklas 2668       name="mean"
2959 27 Nov 06 nicklas 2669       title="Mean FG - Mean BG"
2959 27 Nov 06 nicklas 2670       description="Subtract mean background from mean foreground"
2959 27 Nov 06 nicklas 2671       >
2959 27 Nov 06 nicklas 2672       <formula 
2959 27 Nov 06 nicklas 2673         channel="1"
2959 27 Nov 06 nicklas 2674         expression="raw('SignalMean_Cy3') - raw('BackgroundMean_Cy3')"
2959 27 Nov 06 nicklas 2675       />
2959 27 Nov 06 nicklas 2676       <formula 
2959 27 Nov 06 nicklas 2677         channel="2"
2959 27 Nov 06 nicklas 2678         expression="raw('SignalMean_Cy5') - raw('BackgroundMean_Cy5')"
2959 27 Nov 06 nicklas 2679       />
2959 27 Nov 06 nicklas 2680     </intensity-formula>
2959 27 Nov 06 nicklas 2681     <intensity-formula
2959 27 Nov 06 nicklas 2682       name="median"
2959 27 Nov 06 nicklas 2683       title="Median FG - Median BG"
2959 27 Nov 06 nicklas 2684       description="Subtract meadian background from median foreground"
2959 27 Nov 06 nicklas 2685       >
2959 27 Nov 06 nicklas 2686       <formula 
2959 27 Nov 06 nicklas 2687         channel="1"
2959 27 Nov 06 nicklas 2688         expression="raw('SignalMedian_Cy3') - raw('BackgroundMedian_Cy3')"
2959 27 Nov 06 nicklas 2689       />
2959 27 Nov 06 nicklas 2690       <formula 
2959 27 Nov 06 nicklas 2691         channel="2"
2959 27 Nov 06 nicklas 2692         expression="raw('SignalMedian_Cy5') - raw('BackgroundMedian_Cy5')"
2959 27 Nov 06 nicklas 2693       />
2959 27 Nov 06 nicklas 2694     </intensity-formula>
2959 27 Nov 06 nicklas 2695     <intensity-formula
2959 27 Nov 06 nicklas 2696       name="medianmean"
2959 27 Nov 06 nicklas 2697       title="Median FG - Mean BG"
2959 27 Nov 06 nicklas 2698       description="Subtract mean background from median foreground"
2959 27 Nov 06 nicklas 2699       >
2959 27 Nov 06 nicklas 2700       <formula 
2959 27 Nov 06 nicklas 2701         channel="1"
2959 27 Nov 06 nicklas 2702         expression="raw('SignalMedian_Cy3') - raw('BackgroundMean_Cy3')"
2959 27 Nov 06 nicklas 2703       />
2959 27 Nov 06 nicklas 2704       <formula 
2959 27 Nov 06 nicklas 2705         channel="2"
2959 27 Nov 06 nicklas 2706         expression="raw('SignalMedian_Cy5') - raw('BackgroundMean_Cy5')"
2959 27 Nov 06 nicklas 2707       />
2959 27 Nov 06 nicklas 2708     </intensity-formula>
2959 27 Nov 06 nicklas 2709     <intensity-formula
2959 27 Nov 06 nicklas 2710       name="meanmedian"
2959 27 Nov 06 nicklas 2711       title="Mean FG - Median BG"
2959 27 Nov 06 nicklas 2712       description="Subtract median background from mean foreground"
2959 27 Nov 06 nicklas 2713       >
2959 27 Nov 06 nicklas 2714       <formula 
2959 27 Nov 06 nicklas 2715         channel="1"
2959 27 Nov 06 nicklas 2716         expression="raw('SignalMean_Cy3') - raw('BackgroundMedian_Cy3')"
2959 27 Nov 06 nicklas 2717       />
2959 27 Nov 06 nicklas 2718       <formula 
2959 27 Nov 06 nicklas 2719         channel="2"
2959 27 Nov 06 nicklas 2720         expression="raw('SignalMean_Cy5') - raw('BackgroundMedian_Cy5')"
2959 27 Nov 06 nicklas 2721       />
2959 27 Nov 06 nicklas 2722     </intensity-formula>
2959 27 Nov 06 nicklas 2723     <intensity-formula
2959 27 Nov 06 nicklas 2724       name="meanfg"
2959 27 Nov 06 nicklas 2725       title="Mean FG"
2959 27 Nov 06 nicklas 2726       description="Mean foreground"
2959 27 Nov 06 nicklas 2727       >
2959 27 Nov 06 nicklas 2728       <formula 
2959 27 Nov 06 nicklas 2729         channel="1"
2959 27 Nov 06 nicklas 2730         expression="raw('SignalMean_Cy3')"
2959 27 Nov 06 nicklas 2731       />
2959 27 Nov 06 nicklas 2732       <formula 
2959 27 Nov 06 nicklas 2733         channel="2"
2959 27 Nov 06 nicklas 2734         expression="raw('SignalMean_Cy5')"
2959 27 Nov 06 nicklas 2735       />
2959 27 Nov 06 nicklas 2736     </intensity-formula>
2959 27 Nov 06 nicklas 2737     <intensity-formula
2959 27 Nov 06 nicklas 2738       name="medianfg"
2959 27 Nov 06 nicklas 2739       title="Median FG"
2959 27 Nov 06 nicklas 2740       description="Median foreground"
2959 27 Nov 06 nicklas 2741       >
2959 27 Nov 06 nicklas 2742       <formula 
2959 27 Nov 06 nicklas 2743         channel="1"
2959 27 Nov 06 nicklas 2744         expression="raw('SignalMedian_Cy3')"
2959 27 Nov 06 nicklas 2745       />
2959 27 Nov 06 nicklas 2746       <formula 
2959 27 Nov 06 nicklas 2747         channel="2"
2959 27 Nov 06 nicklas 2748         expression="raw('SignalMedian_Cy5')"
2959 27 Nov 06 nicklas 2749       />
2959 27 Nov 06 nicklas 2750     </intensity-formula>
2959 27 Nov 06 nicklas 2751     <intensity-formula
2959 27 Nov 06 nicklas 2752       name="medianfgmeanmedianbg"
2959 27 Nov 06 nicklas 2753       title="Median FG - Mean(Median BG)"
2959 27 Nov 06 nicklas 2754       description="Subtract mean of median backgrounds from median foreground"
2959 27 Nov 06 nicklas 2755       >
2959 27 Nov 06 nicklas 2756       <formula 
2959 27 Nov 06 nicklas 2757         channel="1"
2959 27 Nov 06 nicklas 2758         expression="raw('SignalMedian_Cy3') - mean('BackgroundMedian_Cy3')"
2959 27 Nov 06 nicklas 2759       />
2959 27 Nov 06 nicklas 2760       <formula 
2959 27 Nov 06 nicklas 2761         channel="2"
2959 27 Nov 06 nicklas 2762         expression="raw('SignalMedian_Cy5') - mean('BackgroundMedian_Cy5')"
2959 27 Nov 06 nicklas 2763       />
2959 27 Nov 06 nicklas 2764     </intensity-formula>
2959 27 Nov 06 nicklas 2765     <intensity-formula
2959 27 Nov 06 nicklas 2766       name="meanfgmeanmeanbg"
2959 27 Nov 06 nicklas 2767       title="Mean FG - Mean(Mean BG)"
2959 27 Nov 06 nicklas 2768       description="Subtract mean of mean backgrounds from mean foreground"
2959 27 Nov 06 nicklas 2769       >
2959 27 Nov 06 nicklas 2770       <formula 
2959 27 Nov 06 nicklas 2771         channel="1"
2959 27 Nov 06 nicklas 2772         expression="raw('SignalMean_Cy3') - mean('BackgroundMean_Cy3')"
2959 27 Nov 06 nicklas 2773       />
2959 27 Nov 06 nicklas 2774       <formula 
2959 27 Nov 06 nicklas 2775         channel="2"
2959 27 Nov 06 nicklas 2776         expression="raw('SignalMean_Cy5') - mean('BackgroundMean_Cy5')"
2959 27 Nov 06 nicklas 2777       />
2959 27 Nov 06 nicklas 2778     </intensity-formula>
2959 27 Nov 06 nicklas 2779     <intensity-formula
2959 27 Nov 06 nicklas 2780       name="medianfgmeanmeanbg"
2959 27 Nov 06 nicklas 2781       title="Median FG - Mean(Mean BG)"
2959 27 Nov 06 nicklas 2782       description="Subtract mean of mean backgrounds from median foreground"
2959 27 Nov 06 nicklas 2783       >
2959 27 Nov 06 nicklas 2784       <formula 
2959 27 Nov 06 nicklas 2785         channel="1"
2959 27 Nov 06 nicklas 2786         expression="raw('SignalMedian_Cy3') - mean('BackgroundMean_Cy3')"
2959 27 Nov 06 nicklas 2787       />
2959 27 Nov 06 nicklas 2788       <formula 
2959 27 Nov 06 nicklas 2789         channel="2"
2959 27 Nov 06 nicklas 2790         expression="raw('SignalMedian_Cy5') - mean('BackgroundMean_Cy5')"
2959 27 Nov 06 nicklas 2791       />
2959 27 Nov 06 nicklas 2792     </intensity-formula>
2959 27 Nov 06 nicklas 2793     <intensity-formula
2959 27 Nov 06 nicklas 2794       name="meanfgmeanmedianbg"
2959 27 Nov 06 nicklas 2795       title="Mean FG - Mean(Median BG)"
2959 27 Nov 06 nicklas 2796       description="Subtract mean of median backgrounds from mean foreground"
2959 27 Nov 06 nicklas 2797       >
2959 27 Nov 06 nicklas 2798       <formula 
2959 27 Nov 06 nicklas 2799         channel="1"
2959 27 Nov 06 nicklas 2800         expression="raw('SignalMean_Cy3') - mean('BackgroundMedian_Cy3')"
2959 27 Nov 06 nicklas 2801       />
2959 27 Nov 06 nicklas 2802       <formula 
2959 27 Nov 06 nicklas 2803         channel="2"
2959 27 Nov 06 nicklas 2804         expression="raw('SignalMean_Cy5') - mean('BackgroundMedian_Cy5')"
2959 27 Nov 06 nicklas 2805       />
2959 27 Nov 06 nicklas 2806     </intensity-formula>
2959 27 Nov 06 nicklas 2807   </raw-data-type>
2959 27 Nov 06 nicklas 2808   
2959 27 Nov 06 nicklas 2809   <raw-data-type
2959 27 Nov 06 nicklas 2810     id="quantarraybiotin"
2959 27 Nov 06 nicklas 2811     channels="1"
2959 27 Nov 06 nicklas 2812     name="QuantArray Biotin"
2959 27 Nov 06 nicklas 2813     table="RawDataQuantArrayBiotin"
2959 27 Nov 06 nicklas 2814     >
2959 27 Nov 06 nicklas 2815     <property
2959 27 Nov 06 nicklas 2816       name="Number"
2959 27 Nov 06 nicklas 2817       title="Number"
2959 27 Nov 06 nicklas 2818       description="Number."
2959 27 Nov 06 nicklas 2819       column="number"
2959 27 Nov 06 nicklas 2820       type="int"
4027 30 Nov 07 enell 2821       averagemethod="none"
2959 27 Nov 06 nicklas 2822     />
2959 27 Nov 06 nicklas 2823     <property
2959 27 Nov 06 nicklas 2824       name="BiotinIntensity"
2959 27 Nov 06 nicklas 2825       title="Intensity"
2959 27 Nov 06 nicklas 2826       description="Mean pixel biotin foreground intensity in biotin channel."
2959 27 Nov 06 nicklas 2827       column="intensity"
2959 27 Nov 06 nicklas 2828       channel="1"
2959 27 Nov 06 nicklas 2829       type="float"
4027 30 Nov 07 enell 2830       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2831     />
2959 27 Nov 06 nicklas 2832     <property
2959 27 Nov 06 nicklas 2833       name="BiotinBackground"
2959 27 Nov 06 nicklas 2834       title="Background"
2959 27 Nov 06 nicklas 2835       description="Mean pixel biotin background intensity in biotin channel."
2959 27 Nov 06 nicklas 2836       column="background"
2959 27 Nov 06 nicklas 2837       channel="1"
2959 27 Nov 06 nicklas 2838       type="float"
4027 30 Nov 07 enell 2839       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2840     />
2959 27 Nov 06 nicklas 2841     <property
2959 27 Nov 06 nicklas 2842       name="BiotinDiameter"
2959 27 Nov 06 nicklas 2843       title="Diameter"
2959 27 Nov 06 nicklas 2844       description="Average diameter of the spot (in microns). Used to determine whether the spot is close to the expected size or is perhaps an artifact on the slide."
2959 27 Nov 06 nicklas 2845       column="diameter"
2959 27 Nov 06 nicklas 2846       channel="1"
2959 27 Nov 06 nicklas 2847       type="float"
4027 30 Nov 07 enell 2848       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2849     />
2959 27 Nov 06 nicklas 2850     <property
2959 27 Nov 06 nicklas 2851       name="BiotinArea"
2959 27 Nov 06 nicklas 2852       title="Area"
2959 27 Nov 06 nicklas 2853       description="The area of the spot given as the number of pixels (in sq. microns). Used to determine whether the spot is close to the expected size or is an artifact on the slide."
2959 27 Nov 06 nicklas 2854       column="area"
2959 27 Nov 06 nicklas 2855       channel="1"
2959 27 Nov 06 nicklas 2856       type="int"
4027 30 Nov 07 enell 2857       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2858     />
2959 27 Nov 06 nicklas 2859     <property
2959 27 Nov 06 nicklas 2860       name="BiotinFootprint"
2959 27 Nov 06 nicklas 2861       title="Footprint"
2959 27 Nov 06 nicklas 2862       description="The distance between the expected position of a spot and its actual measured position (in microns)."
2959 27 Nov 06 nicklas 2863       column="footprint"
2959 27 Nov 06 nicklas 2864       channel="1"
2959 27 Nov 06 nicklas 2865       type="float"
4027 30 Nov 07 enell 2866       averagemethod="none"
2959 27 Nov 06 nicklas 2867     />
2959 27 Nov 06 nicklas 2868     <property
2959 27 Nov 06 nicklas 2869       name="BiotinCircularity"
2959 27 Nov 06 nicklas 2870       title="Circularity"
2959 27 Nov 06 nicklas 2871       description="Reports the degree to which a spot is close to a perfect circle. This measurement is used to determine the print quality of the microarray."
2959 27 Nov 06 nicklas 2872       column="cirularity"
2959 27 Nov 06 nicklas 2873       channel="1"
2959 27 Nov 06 nicklas 2874       type="float"
4027 30 Nov 07 enell 2875       averagemethod="none"
2959 27 Nov 06 nicklas 2876     />
2959 27 Nov 06 nicklas 2877     <property
2959 27 Nov 06 nicklas 2878       name="BiotinSpotUniformity"
2959 27 Nov 06 nicklas 2879       title="Spot uniformity"
2959 27 Nov 06 nicklas 2880       description="The uniformity of the pixels used in the spot foreground intensity calculation. This helps in determining the quality of the spot and aids in selecting the correct quantification output method."
2959 27 Nov 06 nicklas 2881       column="uniformity"
2959 27 Nov 06 nicklas 2882       channel="1"
2959 27 Nov 06 nicklas 2883       type="float"
4027 30 Nov 07 enell 2884       averagemethod="none"
2959 27 Nov 06 nicklas 2885     />
2959 27 Nov 06 nicklas 2886     <property
2959 27 Nov 06 nicklas 2887       name="BiotinBkgUniformity"
2959 27 Nov 06 nicklas 2888       title="Background uniformity"
2959 27 Nov 06 nicklas 2889       description="The uniformity of the pixels used in the background intensity calculation."
2959 27 Nov 06 nicklas 2890       column="bg_uniformity"
2959 27 Nov 06 nicklas 2891       channel="1"
2959 27 Nov 06 nicklas 2892       type="float"
4027 30 Nov 07 enell 2893       averagemethod="none"
2959 27 Nov 06 nicklas 2894     />
2959 27 Nov 06 nicklas 2895     <property
2959 27 Nov 06 nicklas 2896       name="BiotinSignalNoiseRatio"
2959 27 Nov 06 nicklas 2897       title="Signal noise ratio"
2959 27 Nov 06 nicklas 2898       description="The ratio of spot intensity to the standard deviation of the local background of all spots in the microarray. Spots with a low Signal/Noise Ratio can be quickly identified for later reviews."
2959 27 Nov 06 nicklas 2899       column="snr"
2959 27 Nov 06 nicklas 2900       channel="1"
2959 27 Nov 06 nicklas 2901       type="float"
4027 30 Nov 07 enell 2902       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 2903     />
2959 27 Nov 06 nicklas 2904     <property
2959 27 Nov 06 nicklas 2905       name="BiotinConfidence"
2959 27 Nov 06 nicklas 2906       title="Confidence"
2959 27 Nov 06 nicklas 2907       description="Confidence."
2959 27 Nov 06 nicklas 2908       column="confidence"
2959 27 Nov 06 nicklas 2909       channel="1"
2959 27 Nov 06 nicklas 2910       type="int"
4027 30 Nov 07 enell 2911       averagemethod="none"
2959 27 Nov 06 nicklas 2912     />
2959 27 Nov 06 nicklas 2913     <property
2959 27 Nov 06 nicklas 2914       name="IgnoreFilter"
2959 27 Nov 06 nicklas 2915       title="Ignore filter"
2959 27 Nov 06 nicklas 2916       description="Whether the feature quantitation is used in down-stream analysis (flagging feature as valid): 0 = feature invalid (null data); 1 = feature valid."
2959 27 Nov 06 nicklas 2917       column="ignore_filter"
2959 27 Nov 06 nicklas 2918       type="int"
4027 30 Nov 07 enell 2919       averagemethod="none"
2959 27 Nov 06 nicklas 2920     />
2959 27 Nov 06 nicklas 2921     <property
2959 27 Nov 06 nicklas 2922       name="BiotinRatio"
2959 27 Nov 06 nicklas 2923       title="Ratio"
2959 27 Nov 06 nicklas 2924       description="The portion of the overall spot fluorescence contributed by biotin channel (normalized so that biotin channel contribution equals 1)."
2959 27 Nov 06 nicklas 2925       column="ratio"
2959 27 Nov 06 nicklas 2926       channel="1"
2959 27 Nov 06 nicklas 2927       type="int"
4027 30 Nov 07 enell 2928       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 2929     />
2959 27 Nov 06 nicklas 2930     <property
2959 27 Nov 06 nicklas 2931       name="BiotinPercent"
2959 27 Nov 06 nicklas 2932       title="Percent"
2959 27 Nov 06 nicklas 2933       description="The portion of the overall spot fluorescence contributed by biotin channel (in percent)."
2959 27 Nov 06 nicklas 2934       column="precent"
2959 27 Nov 06 nicklas 2935       channel="1"
2959 27 Nov 06 nicklas 2936       type="float"
4027 30 Nov 07 enell 2937       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 2938     />
2959 27 Nov 06 nicklas 2939     <property
2959 27 Nov 06 nicklas 2940       name="BiotinDiameterFilter"
2959 27 Nov 06 nicklas 2941       title="Diameter filter"
2959 27 Nov 06 nicklas 2942       description="Biotin diameter filter."
2959 27 Nov 06 nicklas 2943       column="diameter_filter"
2959 27 Nov 06 nicklas 2944       type="int"
4027 30 Nov 07 enell 2945       averagemethod="none"
2959 27 Nov 06 nicklas 2946     />
2959 27 Nov 06 nicklas 2947     <property
2959 27 Nov 06 nicklas 2948       name="BiotinAreaFilter"
2959 27 Nov 06 nicklas 2949       title="Area filter"
2959 27 Nov 06 nicklas 2950       description="Biotin area filter."
2959 27 Nov 06 nicklas 2951       column="area_filter"
2959 27 Nov 06 nicklas 2952       type="int"
4027 30 Nov 07 enell 2953       averagemethod="none"
2959 27 Nov 06 nicklas 2954     />
2959 27 Nov 06 nicklas 2955     <property
2959 27 Nov 06 nicklas 2956       name="BiotinFootprintFilter"
2959 27 Nov 06 nicklas 2957       title="Footprint filter"
2959 27 Nov 06 nicklas 2958       description="Biotin footprint filter."
2959 27 Nov 06 nicklas 2959       column="footprint_filter"
2959 27 Nov 06 nicklas 2960       type="int"
4027 30 Nov 07 enell 2961       averagemethod="none"
2959 27 Nov 06 nicklas 2962     />
2959 27 Nov 06 nicklas 2963     <property
2959 27 Nov 06 nicklas 2964       name="BiotinCircularityFilter"
2959 27 Nov 06 nicklas 2965       title="Circularity filter"
2959 27 Nov 06 nicklas 2966       description="Biotin circularity filter."
2959 27 Nov 06 nicklas 2967       column="circularity_filter"
2959 27 Nov 06 nicklas 2968       type="int"
4027 30 Nov 07 enell 2969       averagemethod="none"
2959 27 Nov 06 nicklas 2970     />
2959 27 Nov 06 nicklas 2971     <property
2959 27 Nov 06 nicklas 2972       name="BiotinSpotUniformityFilter"
2959 27 Nov 06 nicklas 2973       title="Spot uniformity filter"
2959 27 Nov 06 nicklas 2974       description="Biotin spot uniformity filter."
2959 27 Nov 06 nicklas 2975       column="uniformity_filter"
2959 27 Nov 06 nicklas 2976       type="int"
4027 30 Nov 07 enell 2977       averagemethod="none"
2959 27 Nov 06 nicklas 2978     />
2959 27 Nov 06 nicklas 2979     <property
2959 27 Nov 06 nicklas 2980       name="BiotinBkgUniformityFilter"
2959 27 Nov 06 nicklas 2981       title="Background uniformity filter"
2959 27 Nov 06 nicklas 2982       description="Biotin background uniformity filter."
2959 27 Nov 06 nicklas 2983       column="bg_uniformity_filter"
2959 27 Nov 06 nicklas 2984       type="int"
4027 30 Nov 07 enell 2985       averagemethod="none"
2959 27 Nov 06 nicklas 2986     />
2959 27 Nov 06 nicklas 2987     <property
2959 27 Nov 06 nicklas 2988       name="BiotinSignalNoiseRatioFilter"
2959 27 Nov 06 nicklas 2989       title="Signal noise ratio filter"
2959 27 Nov 06 nicklas 2990       description="Biotin signal noise ratio filter."
2959 27 Nov 06 nicklas 2991       column="snr_filter"
2959 27 Nov 06 nicklas 2992       type="int"
2959 27 Nov 06 nicklas 2993     />
2959 27 Nov 06 nicklas 2994     <property
2959 27 Nov 06 nicklas 2995       name="BiotinReplicateFilter"
2959 27 Nov 06 nicklas 2996       title="Replicate filter"
2959 27 Nov 06 nicklas 2997       description="Biotin replicate filter."
2959 27 Nov 06 nicklas 2998       column="replicate_filter"
2959 27 Nov 06 nicklas 2999       type="int"
4027 30 Nov 07 enell 3000       averagemethod="none"
2959 27 Nov 06 nicklas 3001     />
2959 27 Nov 06 nicklas 3002     <intensity-formula
2959 27 Nov 06 nicklas 3003       name="meanfg"
2959 27 Nov 06 nicklas 3004       title="Mean FG"
2959 27 Nov 06 nicklas 3005       description="Mean foreground intensity"
2959 27 Nov 06 nicklas 3006       >
2959 27 Nov 06 nicklas 3007       <formula 
2959 27 Nov 06 nicklas 3008         channel="1"
2959 27 Nov 06 nicklas 3009         expression="raw('intensity')"
2959 27 Nov 06 nicklas 3010       />
2959 27 Nov 06 nicklas 3011     </intensity-formula>
2959 27 Nov 06 nicklas 3012     <intensity-formula
2959 27 Nov 06 nicklas 3013       name="mean"
2959 27 Nov 06 nicklas 3014       title="Mean FG - Mean BG"
2959 27 Nov 06 nicklas 3015       description="Subtract mean background from mean foreground"
2959 27 Nov 06 nicklas 3016       >
2959 27 Nov 06 nicklas 3017       <formula 
2959 27 Nov 06 nicklas 3018         channel="1"
2959 27 Nov 06 nicklas 3019         expression="raw('BiotinIntensity') - raw('BiotinBackground')"
2959 27 Nov 06 nicklas 3020       />
2959 27 Nov 06 nicklas 3021     </intensity-formula>
2959 27 Nov 06 nicklas 3022   </raw-data-type>
2959 27 Nov 06 nicklas 3023   
2959 27 Nov 06 nicklas 3024   <raw-data-type
2959 27 Nov 06 nicklas 3025     id="quantarraycy"
2959 27 Nov 06 nicklas 3026     channels="2"
2959 27 Nov 06 nicklas 3027     name="QuantArray Cy"
2959 27 Nov 06 nicklas 3028     table="RawDataQuantArrayCy"
2959 27 Nov 06 nicklas 3029     >
2959 27 Nov 06 nicklas 3030     <property
2959 27 Nov 06 nicklas 3031       name="Cy3Intensity"
2959 27 Nov 06 nicklas 3032       title="Mean Cy3 intensity"
2959 27 Nov 06 nicklas 3033       description="Mean pixel Cy3 foreground intensity in Channel Cy3."
2959 27 Nov 06 nicklas 3034       column="cy3_mean"
2959 27 Nov 06 nicklas 3035       channel="1"
2959 27 Nov 06 nicklas 3036       type="float"
4027 30 Nov 07 enell 3037       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 3038     />
2959 27 Nov 06 nicklas 3039     <property
2959 27 Nov 06 nicklas 3040       name="Cy3Background"
2959 27 Nov 06 nicklas 3041       title="Mean Cy3 background"
2959 27 Nov 06 nicklas 3042       description="Mean pixel Cy3 background intensity in Channel Cy3."
2959 27 Nov 06 nicklas 3043       column="cy3_mean_bg"
2959 27 Nov 06 nicklas 3044       channel="1"
2959 27 Nov 06 nicklas 3045       type="float"
4027 30 Nov 07 enell 3046       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 3047     />
2959 27 Nov 06 nicklas 3048     <property
2959 27 Nov 06 nicklas 3049       name="Cy3Diameter"
2959 27 Nov 06 nicklas 3050       title="Cy3 spot diameter"
2959 27 Nov 06 nicklas 3051       description="Average diameter of the spot (in microns). Used to determine whether the spot is close to the expected size or is perhaps an artifact on the slide."
2959 27 Nov 06 nicklas 3052       column="cy3_diameter"
2959 27 Nov 06 nicklas 3053       channel="1"
2959 27 Nov 06 nicklas 3054       type="float"
4027 30 Nov 07 enell 3055       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 3056     />
2959 27 Nov 06 nicklas 3057     <property
2959 27 Nov 06 nicklas 3058       name="Cy3Area"
2959 27 Nov 06 nicklas 3059       title="Cy3 spot area"
2959 27 Nov 06 nicklas 3060       description="The area of the spot given as the number of pixels (in sq. microns). Used to determine whether the spot is close to the expected size or is an artifact on the slide."
2959 27 Nov 06 nicklas 3061       column="cy3_area"
2959 27 Nov 06 nicklas 3062       channel="1"
2959 27 Nov 06 nicklas 3063       type="int"
4027 30 Nov 07 enell 3064       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 3065     />
2959 27 Nov 06 nicklas 3066     <property
2959 27 Nov 06 nicklas 3067       name="Cy3Footprint"
2959 27 Nov 06 nicklas 3068       title="Cy3 footprint"
2959 27 Nov 06 nicklas 3069       description="The distance between the expected position of a spot and its actual measured position (in microns)."
2959 27 Nov 06 nicklas 3070       column="cy3_footprint"
2959 27 Nov 06 nicklas 3071       channel="1"
2959 27 Nov 06 nicklas 3072       type="float"
4027 30 Nov 07 enell 3073       averagemethod="none"
2959 27 Nov 06 nicklas 3074     />
2959 27 Nov 06 nicklas 3075     <property
2959 27 Nov 06 nicklas 3076       name="Cy3Circularity"
2959 27 Nov 06 nicklas 3077       title="Cy3 circularity"
2959 27 Nov 06 nicklas 3078       description="Reports the degree to which a spot is close to a perfect circle. This measurement is used to determine the print quality of the microarray."
2959 27 Nov 06 nicklas 3079       column="cy3_circularity"
2959 27 Nov 06 nicklas 3080       channel="1"
2959 27 Nov 06 nicklas 3081       type="float"
4027 30 Nov 07 enell 3082       averagemethod="none"
2959 27 Nov 06 nicklas 3083     />
2959 27 Nov 06 nicklas 3084     <property
2959 27 Nov 06 nicklas 3085       name="Cy3SpotUniformity"
2959 27 Nov 06 nicklas 3086       title="Cy3 spot uniformity"
2959 27 Nov 06 nicklas 3087       description="The uniformity of the pixels used in the spot foreground intensity calculation.This helps in determining the quality of the spot and aids in selecting the correct quantification output method."
2959 27 Nov 06 nicklas 3088       column="cy3_uniformity"
2959 27 Nov 06 nicklas 3089       channel="1"
2959 27 Nov 06 nicklas 3090       type="float"
4027 30 Nov 07 enell 3091       averagemethod="none"
2959 27 Nov 06 nicklas 3092     />
2959 27 Nov 06 nicklas 3093     <property
2959 27 Nov 06 nicklas 3094       name="Cy3BkgUniformity"
2959 27 Nov 06 nicklas 3095       title="Cy3 background uniformity"
2959 27 Nov 06 nicklas 3096       description="The uniformity of the pixels used in the background intensity calculation."
2959 27 Nov 06 nicklas 3097       column="cy3_bg_uniformity"
2959 27 Nov 06 nicklas 3098       channel="1"
2959 27 Nov 06 nicklas 3099       type="float"
4027 30 Nov 07 enell 3100       averagemethod="none"
2959 27 Nov 06 nicklas 3101     />
2959 27 Nov 06 nicklas 3102     <property
2959 27 Nov 06 nicklas 3103       name="Cy3SignalNoiseRatio"
2959 27 Nov 06 nicklas 3104       title="Cy3 signal noise ratio"
2959 27 Nov 06 nicklas 3105       description="The ratio of spot intensity to the standard deviation of the local background of all spots in the microarray. Spots with a low Signal/Noise Ratio can be quickly identified for later reviews."
2959 27 Nov 06 nicklas 3106       column="cy3_snr"
2959 27 Nov 06 nicklas 3107       channel="1"
2959 27 Nov 06 nicklas 3108       type="float"
4027 30 Nov 07 enell 3109       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 3110     />
2959 27 Nov 06 nicklas 3111     <property
2959 27 Nov 06 nicklas 3112       name="Cy3Confidence"
2959 27 Nov 06 nicklas 3113       title="Cy3 confidence"
2959 27 Nov 06 nicklas 3114       description="Unused QuantArray feature, will always = 1."
2959 27 Nov 06 nicklas 3115       column="cy3_confidence"
2959 27 Nov 06 nicklas 3116       channel="2"
2959 27 Nov 06 nicklas 3117       type="int"
4027 30 Nov 07 enell 3118       averagemethod="none"
2959 27 Nov 06 nicklas 3119     />
2959 27 Nov 06 nicklas 3120     <property
2959 27 Nov 06 nicklas 3121       name="Cy5Intensity"
2959 27 Nov 06 nicklas 3122       title="Mean Cy5 intensity"
2959 27 Nov 06 nicklas 3123       description="Mean pixel Cy5 foreground intensity in Channel Cy5."
2959 27 Nov 06 nicklas 3124       column="cy5_mean"
2959 27 Nov 06 nicklas 3125       channel="2"
2959 27 Nov 06 nicklas 3126       type="float"
4027 30 Nov 07 enell 3127       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 3128     />
2959 27 Nov 06 nicklas 3129     <property
2959 27 Nov 06 nicklas 3130       name="Cy5Background"
2959 27 Nov 06 nicklas 3131       title="Mean Cy5 background"
2959 27 Nov 06 nicklas 3132       description="Mean pixel Cy5 background intensity in Channel Cy5."
2959 27 Nov 06 nicklas 3133       column="cy5_mean_bg"
2959 27 Nov 06 nicklas 3134       channel="2"
2959 27 Nov 06 nicklas 3135       type="float"
4027 30 Nov 07 enell 3136       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 3137     />
2959 27 Nov 06 nicklas 3138     <property
2959 27 Nov 06 nicklas 3139       name="Cy5Diameter"
2959 27 Nov 06 nicklas 3140       title="Cy5 spot diameter"
2959 27 Nov 06 nicklas 3141       description="Average diameter of the spot (in microns). Used to determine whether the spot is close to the expected size or is perhaps an artifact on the slide."
2959 27 Nov 06 nicklas 3142       column="cy5_diameter"
2959 27 Nov 06 nicklas 3143       channel="2"
2959 27 Nov 06 nicklas 3144       type="float"
4027 30 Nov 07 enell 3145       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 3146     />
2959 27 Nov 06 nicklas 3147     <property
2959 27 Nov 06 nicklas 3148       name="Cy5Area"
2959 27 Nov 06 nicklas 3149       title="Cy5 spot area"
2959 27 Nov 06 nicklas 3150       description="The area of the spot given as the number of pixels (in sq. microns). Used to determine whether the spot is close to the expected size or is an artifact on the slide."
2959 27 Nov 06 nicklas 3151       column="cy5_area"
2959 27 Nov 06 nicklas 3152       channel="2"
2959 27 Nov 06 nicklas 3153       type="int"
4027 30 Nov 07 enell 3154       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 3155     />
2959 27 Nov 06 nicklas 3156     <property
2959 27 Nov 06 nicklas 3157       name="Cy5Footprint"
2959 27 Nov 06 nicklas 3158       title="Cy5 footprint"
2959 27 Nov 06 nicklas 3159       description="The distance between the expected position of a spot and its actual measured position (in microns)."
2959 27 Nov 06 nicklas 3160       column="cy5_footprint"
2959 27 Nov 06 nicklas 3161       channel="2"
2959 27 Nov 06 nicklas 3162       type="float"
4027 30 Nov 07 enell 3163       averagemethod="none"
2959 27 Nov 06 nicklas 3164     />
2959 27 Nov 06 nicklas 3165     <property
2959 27 Nov 06 nicklas 3166       name="Cy5Circularity"
2959 27 Nov 06 nicklas 3167       title="Cy5 circularity"
2959 27 Nov 06 nicklas 3168       description="Reports the degree to which a spot is close to a perfect circle. This measurement is used to determine the print quality of the microarray."
2959 27 Nov 06 nicklas 3169       column="cy5_circularity"
2959 27 Nov 06 nicklas 3170       channel="2"
2959 27 Nov 06 nicklas 3171       type="float"
4027 30 Nov 07 enell 3172       averagemethod="none"
2959 27 Nov 06 nicklas 3173     />
2959 27 Nov 06 nicklas 3174     <property
2959 27 Nov 06 nicklas 3175       name="Cy5SpotUniformity"
2959 27 Nov 06 nicklas 3176       title="Cy5 spot uniformity"
2959 27 Nov 06 nicklas 3177       description="The uniformity of the pixels used in the spot foreground intensity calculation.This helps in determining the quality of the spot and aids in selecting the correct quantification output method."
2959 27 Nov 06 nicklas 3178       column="cy5_uniformity"
2959 27 Nov 06 nicklas 3179       channel="2"
2959 27 Nov 06 nicklas 3180       type="float"
4027 30 Nov 07 enell 3181       averagemethod="none"
2959 27 Nov 06 nicklas 3182     />
2959 27 Nov 06 nicklas 3183     <property
2959 27 Nov 06 nicklas 3184       name="Cy5BkgUniformity"
2959 27 Nov 06 nicklas 3185       title="Cy5 background uniformity"
2959 27 Nov 06 nicklas 3186       description="The uniformity of the pixels used in the background intensity calculation."
2959 27 Nov 06 nicklas 3187       column="cy5_bg_uniformity"
2959 27 Nov 06 nicklas 3188       channel="2"
2959 27 Nov 06 nicklas 3189       type="float"
4027 30 Nov 07 enell 3190       averagemethod="none"
2959 27 Nov 06 nicklas 3191     />
2959 27 Nov 06 nicklas 3192     <property
2959 27 Nov 06 nicklas 3193       name="Cy5SignalNoiseRatio"
2959 27 Nov 06 nicklas 3194       title="Cy5 signal noise ratio"
2959 27 Nov 06 nicklas 3195       description="The ratio of spot intensity to the standard deviation of the local background of all spots in the microarray. Spots with a low Signal/Noise Ratio can be quickly identified for later reviews."
2959 27 Nov 06 nicklas 3196       column="cy5_snr"
2959 27 Nov 06 nicklas 3197       channel="2"
2959 27 Nov 06 nicklas 3198       type="float"
4027 30 Nov 07 enell 3199       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 3200     />
2959 27 Nov 06 nicklas 3201     <property
2959 27 Nov 06 nicklas 3202       name="Cy5Confidence"
2959 27 Nov 06 nicklas 3203       title="Cy5 confidence"
2959 27 Nov 06 nicklas 3204       description="Unused QuantArray feature, will always = 1."
2959 27 Nov 06 nicklas 3205       column="cy5_confidence"
2959 27 Nov 06 nicklas 3206       channel="2"
2959 27 Nov 06 nicklas 3207       type="int"
4027 30 Nov 07 enell 3208       averagemethod="none"
2959 27 Nov 06 nicklas 3209     />
2959 27 Nov 06 nicklas 3210     <property
2959 27 Nov 06 nicklas 3211       name="IgnoreFilter"
2959 27 Nov 06 nicklas 3212       title="Ignore filter"
2959 27 Nov 06 nicklas 3213       description="Whether the feature quantitation is used in down-stream analysis (flagging feature as valid): 0 = feature invalid (null data); 1 = feature valid."
2959 27 Nov 06 nicklas 3214       column="ignore_filter"
2959 27 Nov 06 nicklas 3215       type="int"
4027 30 Nov 07 enell 3216       averagemethod="none"
2959 27 Nov 06 nicklas 3217     />
2959 27 Nov 06 nicklas 3218     <property
2959 27 Nov 06 nicklas 3219       name="Cy3Ratio"
2959 27 Nov 06 nicklas 3220       title="Cy3 ratio"
2959 27 Nov 06 nicklas 3221       description="The portion of the overall spot fluorescence contributed by channel Cy3 (normalized so that channel Cy3 contribution equals 1)."
2959 27 Nov 06 nicklas 3222       column="cy3_ratio"
2959 27 Nov 06 nicklas 3223       channel="1"
2959 27 Nov 06 nicklas 3224       type="float"
4027 30 Nov 07 enell 3225       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 3226     />
2959 27 Nov 06 nicklas 3227     <property
2959 27 Nov 06 nicklas 3228       name="Cy3Percent"
2959 27 Nov 06 nicklas 3229       title="Cy3 precent"
2959 27 Nov 06 nicklas 3230       description="The portion of the overall spot fluorescence contributed by channel Cy3 (in percent)."
2959 27 Nov 06 nicklas 3231       column="cy3_percent"
2959 27 Nov 06 nicklas 3232       channel="1"
2959 27 Nov 06 nicklas 3233       type="float"
2959 27 Nov 06 nicklas 3234     />
2959 27 Nov 06 nicklas 3235     <property
2959 27 Nov 06 nicklas 3236       name="Cy3SignalNoiseRatioFilter"
2959 27 Nov 06 nicklas 3237       title="Cy3 signal noise ratio filter"
2959 27 Nov 06 nicklas 3238       description="Cy3 signal noise ratio filter"
2959 27 Nov 06 nicklas 3239       column="cy3_snr_filter"
2959 27 Nov 06 nicklas 3240       channel="1"
2959 27 Nov 06 nicklas 3241       type="float"
4027 30 Nov 07 enell 3242       averagemethod="none"
2959 27 Nov 06 nicklas 3243     />
2959 27 Nov 06 nicklas 3244     <property
2959 27 Nov 06 nicklas 3245       name="Cy5Ratio"
2959 27 Nov 06 nicklas 3246       title="Cy5 ratio"
2959 27 Nov 06 nicklas 3247       description="The portion of the overall spot fluorescence contributed by channel Cy5 (normalized so that channel Cy5 contribution equals 1)."
2959 27 Nov 06 nicklas 3248       column="cy5_ratio"
2959 27 Nov 06 nicklas 3249       channel="2"
2959 27 Nov 06 nicklas 3250       type="float"
4027 30 Nov 07 enell 3251       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 3252     />
2959 27 Nov 06 nicklas 3253     <property
2959 27 Nov 06 nicklas 3254       name="Cy5Percent"
2959 27 Nov 06 nicklas 3255       title="Cy5 precent"
2959 27 Nov 06 nicklas 3256       description="The portion of the overall spot fluorescence contributed by channel Cy5 (in percent)."
2959 27 Nov 06 nicklas 3257       column="cy5_percent"
2959 27 Nov 06 nicklas 3258       channel="2"
2959 27 Nov 06 nicklas 3259       type="float"
4027 30 Nov 07 enell 3260       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 3261     />
2959 27 Nov 06 nicklas 3262     <property
2959 27 Nov 06 nicklas 3263       name="Cy5SignalNoiseRatioFilter"
2959 27 Nov 06 nicklas 3264       title="Cy5 signal noise ratio filter"
2959 27 Nov 06 nicklas 3265       description="Cy5 signal noise ratio filter"
2959 27 Nov 06 nicklas 3266       column="cy5_snr_filter"
2959 27 Nov 06 nicklas 3267       channel="2"
2959 27 Nov 06 nicklas 3268       type="float"
4027 30 Nov 07 enell 3269       averagemethod="none"
2959 27 Nov 06 nicklas 3270     />
2959 27 Nov 06 nicklas 3271     <property
2959 27 Nov 06 nicklas 3272       name="log_normalised"
2959 27 Nov 06 nicklas 3273       title="Normalized ratio"
2959 27 Nov 06 nicklas 3274       description="Ratio = log2 Cy5 - log2 Cy3, for dyeswap ratio *-1"
2959 27 Nov 06 nicklas 3275       column="log_normalised"
2959 27 Nov 06 nicklas 3276       type="float"
4027 30 Nov 07 enell 3277       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 3278     />
2959 27 Nov 06 nicklas 3279     <intensity-formula
2959 27 Nov 06 nicklas 3280       name="meanfg"
2959 27 Nov 06 nicklas 3281       title="Mean FG"
2959 27 Nov 06 nicklas 3282       description="Mean foreground intensity"
2959 27 Nov 06 nicklas 3283       >
2959 27 Nov 06 nicklas 3284       <formula 
2959 27 Nov 06 nicklas 3285         channel="1"
2959 27 Nov 06 nicklas 3286         expression="raw('Cy3Intensity')"
2959 27 Nov 06 nicklas 3287       />
2959 27 Nov 06 nicklas 3288       <formula 
2959 27 Nov 06 nicklas 3289         channel="2"
2959 27 Nov 06 nicklas 3290         expression="raw('Cy5Intensity')"
2959 27 Nov 06 nicklas 3291       />
2959 27 Nov 06 nicklas 3292     </intensity-formula>
2959 27 Nov 06 nicklas 3293     <intensity-formula
2959 27 Nov 06 nicklas 3294       name="mean"
2959 27 Nov 06 nicklas 3295       title="Mean FG - Mean BG"
2959 27 Nov 06 nicklas 3296       description="Subtract mean background from mean foreground"
2959 27 Nov 06 nicklas 3297       >
2959 27 Nov 06 nicklas 3298       <formula 
2959 27 Nov 06 nicklas 3299         channel="1"
2959 27 Nov 06 nicklas 3300         expression="raw('Cy3Intensity') - raw('Cy3Background')"
2959 27 Nov 06 nicklas 3301       />
2959 27 Nov 06 nicklas 3302       <formula 
2959 27 Nov 06 nicklas 3303         channel="2"
2959 27 Nov 06 nicklas 3304         expression="raw('Cy5Intensity') - raw('Cy5Background')"
2959 27 Nov 06 nicklas 3305       />
2959 27 Nov 06 nicklas 3306     </intensity-formula>
2959 27 Nov 06 nicklas 3307   </raw-data-type>
2959 27 Nov 06 nicklas 3308   
2959 27 Nov 06 nicklas 3309   <raw-data-type
2959 27 Nov 06 nicklas 3310     id="spotfinder"
2959 27 Nov 06 nicklas 3311     channels="2"
2959 27 Nov 06 nicklas 3312     name="Spotfinder"
2959 27 Nov 06 nicklas 3313     table="RawDataSpotfinder"
2959 27 Nov 06 nicklas 3314     >
2959 27 Nov 06 nicklas 3315     <property
2959 27 Nov 06 nicklas 3316       name="intA"
2959 27 Nov 06 nicklas 3317       title="Intensity A"
2959 27 Nov 06 nicklas 3318       description="Spot intensity in channel A corrected for background."
2959 27 Nov 06 nicklas 3319       column="int_a"
2959 27 Nov 06 nicklas 3320       type="int"
2959 27 Nov 06 nicklas 3321       channel="1"
4027 30 Nov 07 enell 3322       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 3323     />
2959 27 Nov 06 nicklas 3324     <property
2959 27 Nov 06 nicklas 3325       name="intB"
2959 27 Nov 06 nicklas 3326       title="Intensity B"
2959 27 Nov 06 nicklas 3327       description="Spot intensity in channel B corrected for background."
2959 27 Nov 06 nicklas 3328       column="int_b"
2959 27 Nov 06 nicklas 3329       type="int"
2959 27 Nov 06 nicklas 3330       channel="2"
4027 30 Nov 07 enell 3331       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 3332     />
2959 27 Nov 06 nicklas 3333     <property
2959 27 Nov 06 nicklas 3334       name="meanRatio"
2959 27 Nov 06 nicklas 3335       title="Mean ratio"
2959 27 Nov 06 nicklas 3336       description="Spot mean ratio."
2959 27 Nov 06 nicklas 3337       column="mean_ratio"
2959 27 Nov 06 nicklas 3338       type="float"
4027 30 Nov 07 enell 3339       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 3340     />
2959 27 Nov 06 nicklas 3341     <property
2959 27 Nov 06 nicklas 3342       name="area"
2959 27 Nov 06 nicklas 3343       title="Area"
2959 27 Nov 06 nicklas 3344       description="Spot total area in pixels."
2959 27 Nov 06 nicklas 3345       column="area"
2959 27 Nov 06 nicklas 3346       type="int"
4027 30 Nov 07 enell 3347       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 3348     />
2959 27 Nov 06 nicklas 3349     <property
2959 27 Nov 06 nicklas 3350       name="saturation"
2959 27 Nov 06 nicklas 3351       title="Saturation factor"
2959 27 Nov 06 nicklas 3352       description="Spot saturation factor. This measure shows the percentage of non-saturated pixels in the spot used for integration."
2959 27 Nov 06 nicklas 3353       column="saturation"
2959 27 Nov 06 nicklas 3354       type="float"
4027 30 Nov 07 enell 3355       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 3356     />
2959 27 Nov 06 nicklas 3357     <property
2959 27 Nov 06 nicklas 3358       name="medianRatio"
2959 27 Nov 06 nicklas 3359       title="Median ratio"
2959 27 Nov 06 nicklas 3360       description="Spot median ratio."
2959 27 Nov 06 nicklas 3361       column="median_ratio"
2959 27 Nov 06 nicklas 3362       type="float"
4027 30 Nov 07 enell 3363       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 3364     />
2959 27 Nov 06 nicklas 3365     <property
2959 27 Nov 06 nicklas 3366       name="modeRatio"
2959 27 Nov 06 nicklas 3367       title="Mode ratio"
2959 27 Nov 06 nicklas 3368       description="Spot mode ratio."
2959 27 Nov 06 nicklas 3369       column="mode_ratio"
2959 27 Nov 06 nicklas 3370       type="float"
4027 30 Nov 07 enell 3371       averagemethod="geometric_mean"
2959 27 Nov 06 nicklas 3372     />
2959 27 Nov 06 nicklas 3373     <property
2959 27 Nov 06 nicklas 3374       name="bgA"
2959 27 Nov 06 nicklas 3375       title="Background A"
2959 27 Nov 06 nicklas 3376       description="Spot background in channel A."
2959 27 Nov 06 nicklas 3377       column="bg_a"
2959 27 Nov 06 nicklas 3378       channel="1"
2959 27 Nov 06 nicklas 3379       type="int"
4027 30 Nov 07 enell 3380       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 3381     />
2959 27 Nov 06 nicklas 3382     <property
2959 27 Nov 06 nicklas 3383       name="bgB"
2959 27 Nov 06 nicklas 3384       title="Background B"
2959 27 Nov 06 nicklas 3385       description="Spot background in channel B."
2959 27 Nov 06 nicklas 3386       column="bg_b"
2959 27 Nov 06 nicklas 3387       channel="2"
2959 27 Nov 06 nicklas 3388       type="int"
4027 30 Nov 07 enell 3389       averagemethod="arithmetic_mean"
2959 27 Nov 06 nicklas 3390     />
2959 27 Nov 06 nicklas 3391     <property
2959 27 Nov 06 nicklas 3392       name="flagA"
2959 27 Nov 06 nicklas 3393       title="Flag A"
2959 27 Nov 06 nicklas 3394       description="Spot flag in channel A. This flag is set by QC filter."
2959 27 Nov 06 nicklas 3395       column="flag_a"
2959 27 Nov 06 nicklas 3396       channel="1"
2959 27 Nov 06 nicklas 3397       type="string"
4027 30 Nov 07 enell 3398       averagemethod="none"
2959 27 Nov 06 nicklas 3399     />
2959 27 Nov 06 nicklas 3400     <property
2959 27 Nov 06 nicklas 3401       name="flagB"
2959 27 Nov 06 nicklas 3402       title="Flag B"
2959 27 Nov 06 nicklas 3403       description="Spot flag in channel B. This flag is set by QC filter."
2959 27 Nov 06 nicklas 3404       column="flag_b"
2959 27 Nov 06 nicklas 3405       channel="2"
2959 27 Nov 06 nicklas 3406       type="string"
4027 30 Nov 07 enell 3407       averagemethod="none"
2959 27 Nov 06 nicklas 3408     />
2959 27 Nov 06 nicklas 3409     <property
2959 27 Nov 06 nicklas 3410       name="qcA"
2959 27 Nov 06 nicklas 3411       title="Spot QC score A"
2959 27 Nov 06 nicklas 3412       description="Spot QC score in channel A. This is a geometric mean of shape and S/N QC scores in channel A. S/N QC score is calculated as percentage of pixels in a spot with values higher than 2*median(local BKG). Spot shape QC score is defined as ratio of spot area to spot perimeter scaled into the range between 0 and 1."
2959 27 Nov 06 nicklas 3413       column="qc_a"
2959 27 Nov 06 nicklas 3414       channel="1"
2959 27 Nov 06 nicklas 3415       type="float"
4027 30 Nov 07 enell 3416       averagemethod="none"
2959 27 Nov 06 nicklas 3417     />
2959 27 Nov 06 nicklas 3418     <property
2959 27 Nov 06 nicklas 3419       name="qcB"
2959 27 Nov 06 nicklas 3420       title="Spot QC score B"
2959 27 Nov 06 nicklas 3421       description="Spot QC score in channel B. This is a geometric mean of shape and S/N QC scores in channel B. S/N QC score is calculated as percentage of pixels in a spot with values higher than 2*median(local BKG). Spot shape QC score is defined as ratio of spot area to spot perimeter scaled into the range between 0 and 1."
2959 27 Nov 06 nicklas 3422       column="qc_b"
2959 27 Nov 06 nicklas 3423       channel="2"
2959 27 Nov 06 nicklas 3424       type="float"
4027 30 Nov 07 enell 3425       averagemethod="none"
2959 27 Nov 06 nicklas 3426     />
2959 27 Nov 06 nicklas 3427     <property
2959 27 Nov 06 nicklas 3428       name="qcTotal"
2959 27 Nov 06 nicklas 3429       title="Total QC"
2959 27 Nov 06 nicklas 3430       description="Spot total QC score. This is a mean of QC scores in channels A and B."
2959 27 Nov 06 nicklas 3431       column="qc_total"
2959 27 Nov 06 nicklas 3432       type="float"
4027 30 Nov 07 enell 3433       averagemethod="none"
2959 27 Nov 06 nicklas 3434     />
2959 27 Nov 06 nicklas 3435     <property
2959 27 Nov 06 nicklas 3436       name="flag"
2959 27 Nov 06 nicklas 3437       title="Flag"
2959 27 Nov 06 nicklas 3438       description="Flag values are generated based on next conditions: A - the number of non-saturated pixels in spot is 0; B- number of non-saturated pixels in spot is between 30 and 50; C- number of non saturated pixels in spot is more then 50; S- fully or partially saturated spot, this is a warning flag. User should evaluate used spot area. X- spot was detected and rejected based on spot shape and spot intensity relative to surrounding background; Z- spot was not detected by the program; Y- spot background is higher than spot intensity."
2959 27 Nov 06 nicklas 3439       column="flag"
2959 27 Nov 06 nicklas 3440       type="string"
4027 30 Nov 07 enell 3441       averagemethod="none"
2959 27 Nov 06 nicklas 3442     />
2959 27 Nov 06 nicklas 3443     <intensity-formula
2959 27 Nov 06 nicklas 3444       name="int"
2959 27 Nov 06 nicklas 3445       title="Spot intensity"
2959 27 Nov 06 nicklas 3446       description="Spot intensity corrected for background."
2959 27 Nov 06 nicklas 3447       >
2959 27 Nov 06 nicklas 3448       <formula 
2959 27 Nov 06 nicklas 3449         channel="1"
2959 27 Nov 06 nicklas 3450         expression="raw('intA')"
2959 27 Nov 06 nicklas 3451       />
2959 27 Nov 06 nicklas 3452       <formula 
2959 27 Nov 06 nicklas 3453         channel="2"
2959 27 Nov 06 nicklas 3454         expression="raw('intB')"
2959 27 Nov 06 nicklas 3455       />
2959 27 Nov 06 nicklas 3456     </intensity-formula>
2959 27 Nov 06 nicklas 3457   </raw-data-type>
3626 03 Aug 07 nicklas 3458   <raw-data-type 
3626 03 Aug 07 nicklas 3459     id="illumina" 
3626 03 Aug 07 nicklas 3460     channels="1" 
3626 03 Aug 07 nicklas 3461     name="Illumina" 
3626 03 Aug 07 nicklas 3462     table="RawDataIllumina">
3626 03 Aug 07 nicklas 3463     <property
3626 03 Aug 07 nicklas 3464       name="MIN_Signal"
3626 03 Aug 07 nicklas 3465       title="MIN_Signal"
3626 03 Aug 07 nicklas 3466       description="Minimum intensity of the gene in the group."
3626 03 Aug 07 nicklas 3467       column="minSignal"
4027 30 Nov 07 enell 3468       type="float"
4027 30 Nov 07 enell 3469       averagemethod="arithmetic_mean"
3626 03 Aug 07 nicklas 3470     />
3626 03 Aug 07 nicklas 3471     <property
3626 03 Aug 07 nicklas 3472       name="AVG_Signal"
3626 03 Aug 07 nicklas 3473       title="AVG_Signal"
3626 03 Aug 07 nicklas 3474       description="Average intensity of the gene in the group."
3626 03 Aug 07 nicklas 3475       column="avgSignal"
4027 30 Nov 07 enell 3476       type="float"
4027 30 Nov 07 enell 3477       averagemethod="arithmetic_mean"
3626 03 Aug 07 nicklas 3478     />
3626 03 Aug 07 nicklas 3479     <property
3626 03 Aug 07 nicklas 3480       name="MAX_Signal"
3626 03 Aug 07 nicklas 3481       title="MAX_Signal"
3626 03 Aug 07 nicklas 3482       description="Maximum intensity of the gene in the group."
3626 03 Aug 07 nicklas 3483       column="maxSignal"
4027 30 Nov 07 enell 3484       type="float"
4027 30 Nov 07 enell 3485       averagemethod="arithmetic_mean"  
3626 03 Aug 07 nicklas 3486     />
3626 03 Aug 07 nicklas 3487     <property
3626 03 Aug 07 nicklas 3488       name="NARRAYS"
3626 03 Aug 07 nicklas 3489       title="NARRAYS"
3626 03 Aug 07 nicklas 3490       description="Number of arrays in the group."
3626 03 Aug 07 nicklas 3491       column="narrays"
4027 30 Nov 07 enell 3492       type="int"
4027 30 Nov 07 enell 3493       averagemethod="arithmetic_mean"
3626 03 Aug 07 nicklas 3494     />
3626 03 Aug 07 nicklas 3495     <property
3626 03 Aug 07 nicklas 3496       name="ARRAY_STDEV"
3626 03 Aug 07 nicklas 3497       title="ARRAY_STDEV"
3626 03 Aug 07 nicklas 3498       description="Standard deviation associated with array-to-array variability within the group (undefined when the group contains a single array)."
3626 03 Aug 07 nicklas 3499       column="arrayStdDev"
4027 30 Nov 07 enell 3500       type="float"
4027 30 Nov 07 enell 3501       averagemethod="arithmetic_mean"
3626 03 Aug 07 nicklas 3502     />
3626 03 Aug 07 nicklas 3503     <property
3626 03 Aug 07 nicklas 3504       name="BEAD_STDEV"
3626 03 Aug 07 nicklas 3505       title="BEAD_STDEV"
3626 03 Aug 07 nicklas 3506       description="Average standard deviation associated with bead-to-bead variability for the arrays in the group."
3626 03 Aug 07 nicklas 3507       column="beadStdDev"
4027 30 Nov 07 enell 3508       type="float"
4027 30 Nov 07 enell 3509       averagemethod="arithmetic_mean"
3626 03 Aug 07 nicklas 3510     />
3626 03 Aug 07 nicklas 3511     <property
3626 03 Aug 07 nicklas 3512       name="Avg_NBEADS"
3626 03 Aug 07 nicklas 3513       title="Avg_NBEADS"
3626 03 Aug 07 nicklas 3514       description="Average number of beads per bead type representing probes for the gene."
3626 03 Aug 07 nicklas 3515       column="avgNBeads"
4027 30 Nov 07 enell 3516       type="int"
4027 30 Nov 07 enell 3517       averagemethod="arithmetic_mean"
3626 03 Aug 07 nicklas 3518     />
3626 03 Aug 07 nicklas 3519     <property
3626 03 Aug 07 nicklas 3520       name="Detection"
3626 03 Aug 07 nicklas 3521       title="Detection"
3626 03 Aug 07 nicklas 3522       description="p-value computed from the background model characterizing chance that the target sequence signal was distinguishable from the negative controls."
3626 03 Aug 07 nicklas 3523       column="detection"
4027 30 Nov 07 enell 3524       type="float"
4027 30 Nov 07 enell 3525       averagemethod="none"
3626 03 Aug 07 nicklas 3526     />
3626 03 Aug 07 nicklas 3527     <intensity-formula
3626 03 Aug 07 nicklas 3528       name="avgSignal"
3626 03 Aug 07 nicklas 3529       title="Average signal"
3626 03 Aug 07 nicklas 3530       description="Average signal as determined by BeadStudio software."
3626 03 Aug 07 nicklas 3531       >
3626 03 Aug 07 nicklas 3532       <formula 
3626 03 Aug 07 nicklas 3533         channel="1"
3626 03 Aug 07 nicklas 3534         expression="raw('AVG_Signal')"
3626 03 Aug 07 nicklas 3535       />
3626 03 Aug 07 nicklas 3536     </intensity-formula>
3626 03 Aug 07 nicklas 3537   </raw-data-type>
5773 29 Sep 11 nicklas 3538   <raw-data-type
5773 29 Sep 11 nicklas 3539     id="cufflinks" 
5773 29 Sep 11 nicklas 3540     channels="1" 
5773 29 Sep 11 nicklas 3541     name="Cufflinks" 
5773 29 Sep 11 nicklas 3542     table="RawDataCufflinks"
5773 29 Sep 11 nicklas 3543     description="Cufflinks isoforms/gene-level expression values in FPKM tracking format">
5773 29 Sep 11 nicklas 3544     <property
5773 29 Sep 11 nicklas 3545       name="coverage"
5773 29 Sep 11 nicklas 3546       title="Coverage"
5773 29 Sep 11 nicklas 3547       description="Estimate for the absolute depth of read coverage across the object."
5773 29 Sep 11 nicklas 3548       column="coverage"
5773 29 Sep 11 nicklas 3549       type="float"
5773 29 Sep 11 nicklas 3550       averagemethod="arithmetic_mean"
5773 29 Sep 11 nicklas 3551     />
5773 29 Sep 11 nicklas 3552     <property
5773 29 Sep 11 nicklas 3553       name="fpkm"
5773 29 Sep 11 nicklas 3554       title="FPKM"
5773 29 Sep 11 nicklas 3555       description="Fragments Per Kilobase of exon per Million fragments mapped."
5773 29 Sep 11 nicklas 3556       column="fpkm"
5773 29 Sep 11 nicklas 3557       type="float"
5773 29 Sep 11 nicklas 3558       averagemethod="geometric_mean"
5773 29 Sep 11 nicklas 3559     />
5773 29 Sep 11 nicklas 3560     <property
5773 29 Sep 11 nicklas 3561       name="fpkm_lo"
5773 29 Sep 11 nicklas 3562       title="FPKM lo"
5773 29 Sep 11 nicklas 3563       description="The lower bound of the 95% confidence interval on the FPKM."
5773 29 Sep 11 nicklas 3564       column="fpkm_lo"
5773 29 Sep 11 nicklas 3565       type="float"
5773 29 Sep 11 nicklas 3566       averagemethod="geometric_mean"
5773 29 Sep 11 nicklas 3567     />
5773 29 Sep 11 nicklas 3568     <property
5773 29 Sep 11 nicklas 3569       name="fpkm_hi"
5773 29 Sep 11 nicklas 3570       title="FPKM hi"
5773 29 Sep 11 nicklas 3571       description="The upper bound of the 95% confidence interval on the FPKM."
5773 29 Sep 11 nicklas 3572       column="fpkm_hi"
5773 29 Sep 11 nicklas 3573       type="float"
5773 29 Sep 11 nicklas 3574       averagemethod="geometric_mean"
5773 29 Sep 11 nicklas 3575     />
5773 29 Sep 11 nicklas 3576     <property
5773 29 Sep 11 nicklas 3577       name="status"
5773 29 Sep 11 nicklas 3578       title="Status"
5773 29 Sep 11 nicklas 3579       description="Quantification status. Can be one of OK (deconvolution successful), LOWDATA (too complex or shallowly sequenced), HIDATA (too many fragments in locus), or FAIL, when an ill-conditioned covariance matrix or other numerical exception prevents deconvolution."
5773 29 Sep 11 nicklas 3580       column="status"
5773 29 Sep 11 nicklas 3581       type="string"
5773 29 Sep 11 nicklas 3582       length="255"
5773 29 Sep 11 nicklas 3583       averagemethod="none"
5773 29 Sep 11 nicklas 3584     />
5773 29 Sep 11 nicklas 3585     <intensity-formula
5773 29 Sep 11 nicklas 3586       name="fpkm"
5773 29 Sep 11 nicklas 3587       title="FPKM"
5773 29 Sep 11 nicklas 3588       description="Fragments Per Kilobase of exon per Million fragments mapped."
5773 29 Sep 11 nicklas 3589       >
5773 29 Sep 11 nicklas 3590       <formula 
5773 29 Sep 11 nicklas 3591         channel="1"
5773 29 Sep 11 nicklas 3592         expression="raw('fpkm')"
5773 29 Sep 11 nicklas 3593       />
5773 29 Sep 11 nicklas 3594     </intensity-formula>
5773 29 Sep 11 nicklas 3595   
5773 29 Sep 11 nicklas 3596   </raw-data-type>
2959 27 Nov 06 nicklas 3597 </raw-data-types>
2959 27 Nov 06 nicklas 3598

Generated on Sat Oct  7 02:26:58 2023 (UTC) by svndigest 0.11.2pre (dev build 1672)