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<?xml version="1.0" encoding="UTF-8" ?> |
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<!DOCTYPE raw-data-types SYSTEM "raw-data-types.dtd" > |
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<!-- |
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$Id$ |
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|
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Copyright (C) 2010 Jari Häkkinen |
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|
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This file is part of the Agilent plug-in package for BASE |
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(net.sf.based.agilent). |
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The package is available at http://baseplugins.thep.lu.se/ |
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BASE main site is http://base.thep.lu.se/ |
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12 |
|
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This is free software; you can redistribute it and/or modify it |
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under the terms of the GNU General Public License as published by |
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the Free Software Foundation; either version 3 of the License, or |
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(at your option) any later version. |
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17 |
|
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The software is distributed in the hope that it will be useful, but |
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WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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General Public License for more details. |
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22 |
|
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You should have received a copy of the GNU General Public License |
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along with this program. If not, see <http://www.gnu.org/licenses/>. |
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--> |
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|
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<raw-data-types> |
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|
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<raw-data-type |
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id="agilent1ch" |
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channels="1" |
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name="AgilentGE1ch" |
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table="RawDataAgilent1ch" |
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> |
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<property |
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name="gSurrogateUsed" |
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title="G surrogate used" |
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description="The green surrogate value used." |
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column="g_surrogate_used" |
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channel="1" |
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type="float" |
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averagemethod="none" |
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/> |
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<property |
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name="gIsFound" |
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title="G is found" |
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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." |
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column="g_is_found" |
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channel="1" |
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type="boolean" |
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averagemethod="none" |
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/> |
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<property |
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name="gProcessedSignal" |
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title="G processed signal" |
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description="The propagated feature signal, per channel, used for computation of log ratio." |
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column="g_processed_signal" |
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channel="1" |
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type="float" |
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averagemethod="arithmetic_mean" |
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/> |
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<property |
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name="gNumPixOLHi" |
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title="G high outlier pixels" |
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description="Number of outlier pixels per feature with intensity > 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." |
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column="g_high_outlier_pixels" |
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channel="1" |
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type="int" |
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averagemethod="arithmetic_mean" |
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/> |
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<property |
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name="gNumPixOLLo" |
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title="G low outlier pixels" |
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description="Number of outlier pixels per feature with intensity < 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." |
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column="g_low_outlier_pixels" |
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channel="1" |
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type="int" |
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averagemethod="arithmetic_mean" |
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/> |
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<property |
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name="gNumPix" |
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title="G pixels" |
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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." |
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column="g_pixels" |
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channel="1" |
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type="int" |
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averagemethod="arithmetic_mean" |
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/> |
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<property |
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name="gMeanSignal" |
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title="G mean signal" |
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description="Raw mean signal of feature in green channel." |
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column="g_mean_signal" |
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channel="1" |
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type="float" |
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averagemethod="arithmetic_mean" |
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/> |
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<property |
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name="gMedianSignal" |
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title="G median signal" |
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description="Raw median signal of feature in green channel." |
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column="g_median_signal" |
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channel="1" |
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type="float" |
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averagemethod="arithmetic_mean" |
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/> |
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<property |
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name="gBGNumPix" |
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title="G background pixels" |
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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." |
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column="g_bg_pixels" |
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channel="1" |
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type="int" |
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averagemethod="arithmetic_mean" |
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/> |
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<property |
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name="gBGMeanSignal" |
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title="G mean background" |
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description="Mean local background signal (local to corresponding feature) computed per channel." |
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column="g_bg_mean_signal" |
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channel="1" |
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type="float" |
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averagemethod="arithmetic_mean" |
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/> |
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<property |
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name="gBGMedianSignal" |
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title="G median background" |
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description="Median local background signal (local to corresponding feature) computed per channel." |
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column="g_bg_median_signal" |
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channel="1" |
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type="float" |
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averagemethod="arithmetic_mean" |
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/> |
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<property |
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name="gNumSatPix" |
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title="G saturated pixels" |
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description="Total number of saturated pixels per feature, computed per channel." |
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column="g_sat_pixels" |
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channel="1" |
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type="int" |
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averagemethod="arithmetic_mean" |
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/> |
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<property |
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name="gIsSaturated" |
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title="G is saturated" |
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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." |
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column="g_is_saturated" |
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channel="1" |
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type="boolean" |
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averagemethod="none" |
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/> |
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<property |
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name="gIsFeatNonUnifOL" |
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title="G non-uniform outlier" |
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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." |
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column="g_nonuniform_outlier" |
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channel="1" |
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type="boolean" |
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averagemethod="none" |
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/> |
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<property |
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name="gIsBGNonUnifOL" |
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title="G bg non-uniform outlier" |
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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." |
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column="g_bg_nonuniform_outlier" |
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channel="1" |
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type="boolean" |
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/> |
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<property |
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name="gIsFeatPopnOL" |
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title="G population outlier" |
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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." |
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column="g_population_outlier" |
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channel="1" |
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type="boolean" |
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/> |
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<property |
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name="gIsBGPopnOL" |
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title="G bg population outlier" |
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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." |
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column="g_bg_population_outlier" |
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channel="1" |
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type="boolean" |
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averagemethod="none" |
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/> |
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<property |
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name="IsManualFlag" |
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title="Manual flag" |
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description="If a feature has been moved manually this flag will be set to 1." |
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column="manual_flag" |
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type="boolean" |
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averagemethod="none" |
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/> |
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<property |
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name="gBGSubSignal" |
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title="G net signal" |
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description="The net green signal following the subtraction of the background from the raw mean green signal." |
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column="g_net_signal" |
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channel="1" |
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type="float" |
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/> |
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<property |
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name="gIsPosAndSignif" |
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title="G > 0 and significant" |
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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." |
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column="g_significant" |
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channel="1" |
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type="boolean" |
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averagemethod="none" |
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/> |
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<property |
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name="gPValFeatEqBG" |
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title="G p-value" |
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description="P-value from t-test of significance between green Mean signal and green background." |
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column="g_pvalue" |
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channel="1" |
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type="float" |
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averagemethod="none" |
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/> |
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<property |
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name="gNumBGUsed" |
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title="G background pixels" |
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description="A count of the number of background pixels used in the green channel." |
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column="g_numbg_used" |
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channel="1" |
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type="int" |
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averagemethod="arithmetic_mean" |
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/> |
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06 Mar 10 |
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229 |
<property |
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name="gIsWellAboveBG" |
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06 Mar 10 |
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title="G well above bg" |
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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." |
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column="g_above_bg" |
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channel="1" |
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type="boolean" |
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averagemethod="none" |
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/> |
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<property |
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name="gBGUsed" |
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title="G bg used" |
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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." |
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column="g_bg_used" |
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channel="1" |
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type="float" |
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averagemethod="arithmetic_mean" |
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/> |
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<property |
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name="ErrorModel" |
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title="Error model" |
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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." |
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column="error_model" |
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type="int" |
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averagemethod="none" |
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/> |
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06 Mar 10 |
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<property |
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name="gSpatialDetrendIsInFilteredSet" |
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title="G spatial trend" |
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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." |
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column="g_spatial_trend" |
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channel="1" |
1199 |
06 Mar 10 |
jari |
261 |
type="boolean" |
1199 |
06 Mar 10 |
jari |
262 |
averagemethod="none" |
1199 |
06 Mar 10 |
jari |
263 |
/> |
1199 |
06 Mar 10 |
jari |
264 |
<property |
1199 |
06 Mar 10 |
jari |
265 |
name="gSpatialDetrendSurfaceValue" |
1199 |
06 Mar 10 |
jari |
266 |
title="G surface value" |
1199 |
06 Mar 10 |
jari |
267 |
description="Value of the smoothed surface derived from the set of features that are part of SpatialDetrendIsInFilteredSet." |
1199 |
06 Mar 10 |
jari |
268 |
column="g_surface_value" |
1199 |
06 Mar 10 |
jari |
269 |
channel="1" |
1199 |
06 Mar 10 |
jari |
270 |
type="float" |
1199 |
06 Mar 10 |
jari |
271 |
averagemethod="arithmetic_mean" |
1199 |
06 Mar 10 |
jari |
272 |
/> |
1199 |
06 Mar 10 |
jari |
273 |
<property |
1199 |
06 Mar 10 |
jari |
274 |
name="gPixSDev" |
1199 |
06 Mar 10 |
jari |
275 |
title="G pixel SDev" |
1199 |
06 Mar 10 |
jari |
276 |
description="Standard deviation of all inlier pixels per feature; this is computed independently in each channel." |
1199 |
06 Mar 10 |
jari |
277 |
column="gPixSDev" |
1199 |
06 Mar 10 |
jari |
278 |
type="float" |
1199 |
06 Mar 10 |
jari |
279 |
averagemethod="none" |
1199 |
06 Mar 10 |
jari |
280 |
/> |
1199 |
06 Mar 10 |
jari |
281 |
<property |
1199 |
06 Mar 10 |
jari |
282 |
name="gBGPixSDev" |
1199 |
06 Mar 10 |
jari |
283 |
title="G background pixel SDev" |
1199 |
06 Mar 10 |
jari |
284 |
description="Standard deviation of all inlier pixels per Local BG of each feature, computed independently in each channelStandard deviation of all inlier pixels per Local BG of each feature, computed independently in each channel." |
1199 |
06 Mar 10 |
jari |
285 |
column="gBGPixSDev" |
1199 |
06 Mar 10 |
jari |
286 |
type="float" |
1199 |
06 Mar 10 |
jari |
287 |
averagemethod="none" |
1199 |
06 Mar 10 |
jari |
288 |
/> |
1199 |
06 Mar 10 |
jari |
289 |
<intensity-formula |
1199 |
06 Mar 10 |
jari |
290 |
name="mean" |
1199 |
06 Mar 10 |
jari |
291 |
title="Mean FG - Mean BG" |
1199 |
06 Mar 10 |
jari |
292 |
description="Subtract mean background from mean foreground" |
1199 |
06 Mar 10 |
jari |
293 |
> |
1199 |
06 Mar 10 |
jari |
294 |
<formula channel="1" |
1199 |
06 Mar 10 |
jari |
295 |
expression="raw('gMeanSignal') - raw('gBGMeanSignal')" /> |
1199 |
06 Mar 10 |
jari |
296 |
</intensity-formula> |
1199 |
06 Mar 10 |
jari |
297 |
<intensity-formula |
1199 |
06 Mar 10 |
jari |
298 |
name="median" |
1199 |
06 Mar 10 |
jari |
299 |
title="Median FG - Median BG" |
1199 |
06 Mar 10 |
jari |
300 |
description="Subtract meadian background from median foreground" |
1199 |
06 Mar 10 |
jari |
301 |
> |
1199 |
06 Mar 10 |
jari |
302 |
<formula channel="1" |
1199 |
06 Mar 10 |
jari |
303 |
expression="raw('gMedianSignal') - raw('gBGMedianSignal')" /> |
1199 |
06 Mar 10 |
jari |
304 |
</intensity-formula> |
1199 |
06 Mar 10 |
jari |
305 |
<intensity-formula |
1199 |
06 Mar 10 |
jari |
306 |
name="medianmean" |
1199 |
06 Mar 10 |
jari |
307 |
title="Median FG - Mean BG" |
1199 |
06 Mar 10 |
jari |
308 |
description="Subtract mean background from median foreground" |
1199 |
06 Mar 10 |
jari |
309 |
> |
1199 |
06 Mar 10 |
jari |
310 |
<formula channel="1" |
1199 |
06 Mar 10 |
jari |
311 |
expression="raw('gMedianSignal') - raw('gBGMeanSignal')" /> |
1199 |
06 Mar 10 |
jari |
312 |
</intensity-formula> |
1199 |
06 Mar 10 |
jari |
313 |
<intensity-formula |
1199 |
06 Mar 10 |
jari |
314 |
name="meanmedian" |
1199 |
06 Mar 10 |
jari |
315 |
title="Mean FG - Median BG" |
1199 |
06 Mar 10 |
jari |
316 |
description="Subtract median background from mean foreground" |
1199 |
06 Mar 10 |
jari |
317 |
> |
1199 |
06 Mar 10 |
jari |
318 |
<formula channel="1" |
1199 |
06 Mar 10 |
jari |
319 |
expression="raw('gMeanSignal') - raw('gBGMedianSignal')" /> |
1199 |
06 Mar 10 |
jari |
320 |
</intensity-formula> |
1199 |
06 Mar 10 |
jari |
321 |
<intensity-formula |
1199 |
06 Mar 10 |
jari |
322 |
name="meanfg" |
1199 |
06 Mar 10 |
jari |
323 |
title="Mean FG" |
1199 |
06 Mar 10 |
jari |
324 |
description="Mean foreground" |
1199 |
06 Mar 10 |
jari |
325 |
> |
1199 |
06 Mar 10 |
jari |
326 |
<formula channel="1" |
1199 |
06 Mar 10 |
jari |
327 |
expression="raw('gMeanSignal')" /> |
1199 |
06 Mar 10 |
jari |
328 |
</intensity-formula> |
1199 |
06 Mar 10 |
jari |
329 |
<intensity-formula |
1199 |
06 Mar 10 |
jari |
330 |
name="medianfg" |
1199 |
06 Mar 10 |
jari |
331 |
title="Median FG" |
1199 |
06 Mar 10 |
jari |
332 |
description="Median foreground" |
1199 |
06 Mar 10 |
jari |
333 |
> |
1199 |
06 Mar 10 |
jari |
334 |
<formula channel="1" |
1199 |
06 Mar 10 |
jari |
335 |
expression="raw('gMedianSignal')" /> |
1199 |
06 Mar 10 |
jari |
336 |
</intensity-formula> |
1199 |
06 Mar 10 |
jari |
337 |
<intensity-formula |
1199 |
06 Mar 10 |
jari |
338 |
name="medianfgmeanmedianbg" |
1199 |
06 Mar 10 |
jari |
339 |
title="Median FG - Mean(Median BG)" |
1199 |
06 Mar 10 |
jari |
340 |
description="Subtract mean of median backgrounds from median foreground" |
1199 |
06 Mar 10 |
jari |
341 |
> |
1199 |
06 Mar 10 |
jari |
342 |
<formula channel="1" |
1199 |
06 Mar 10 |
jari |
343 |
expression="raw('gMedianSignal') - mean('gBGMedianSignal')" /> |
1199 |
06 Mar 10 |
jari |
344 |
</intensity-formula> |
1199 |
06 Mar 10 |
jari |
345 |
<intensity-formula |
1199 |
06 Mar 10 |
jari |
346 |
name="meanfgmeanmeanbg" |
1199 |
06 Mar 10 |
jari |
347 |
title="Mean FG - Mean(Mean BG)" |
1199 |
06 Mar 10 |
jari |
348 |
description="Subtract mean of mean backgrounds from mean foreground" |
1199 |
06 Mar 10 |
jari |
349 |
> |
1199 |
06 Mar 10 |
jari |
350 |
<formula channel="1" |
1199 |
06 Mar 10 |
jari |
351 |
expression="raw('gMeanSignal') - mean('gBGMeanSignal')" /> |
1199 |
06 Mar 10 |
jari |
352 |
</intensity-formula> |
1199 |
06 Mar 10 |
jari |
353 |
<intensity-formula |
1199 |
06 Mar 10 |
jari |
354 |
name="medianfgmeanmeanbg" |
1199 |
06 Mar 10 |
jari |
355 |
title="Median FG - Mean(Mean BG)" |
1199 |
06 Mar 10 |
jari |
356 |
description="Subtract mean of mean backgrounds from median foreground" |
1199 |
06 Mar 10 |
jari |
357 |
> |
1199 |
06 Mar 10 |
jari |
358 |
<formula channel="1" |
1199 |
06 Mar 10 |
jari |
359 |
expression="raw('gMedianSignal') - mean('gBGMeanSignal')" /> |
1199 |
06 Mar 10 |
jari |
360 |
</intensity-formula> |
1199 |
06 Mar 10 |
jari |
361 |
<intensity-formula |
1199 |
06 Mar 10 |
jari |
362 |
name="meanfgmeanmedianbg" |
1199 |
06 Mar 10 |
jari |
363 |
title="Mean FG - Mean(Median BG)" |
1199 |
06 Mar 10 |
jari |
364 |
description="Subtract mean of median backgrounds from mean foreground" |
1199 |
06 Mar 10 |
jari |
365 |
> |
1199 |
06 Mar 10 |
jari |
366 |
<formula channel="1" |
1199 |
06 Mar 10 |
jari |
367 |
expression="raw('gMeanSignal') - mean('gBGMedianSignal')" /> |
1199 |
06 Mar 10 |
jari |
368 |
</intensity-formula> |
1199 |
06 Mar 10 |
jari |
369 |
</raw-data-type> |
1199 |
06 Mar 10 |
jari |
370 |
|
1199 |
06 Mar 10 |
jari |
371 |
</raw-data-types> |