3334 |
14 May 07 |
nicklas |
1 |
<?xml version="1.0" encoding="UTF-8"?> |
3334 |
14 May 07 |
nicklas |
2 |
<!DOCTYPE appendix PUBLIC |
3334 |
14 May 07 |
nicklas |
3 |
"-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN" |
3334 |
14 May 07 |
nicklas |
4 |
"../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd"> |
3334 |
14 May 07 |
nicklas |
5 |
<!-- |
3334 |
14 May 07 |
nicklas |
$Id$ |
3334 |
14 May 07 |
nicklas |
7 |
|
3675 |
16 Aug 07 |
jari |
Copyright (C) 2007 Nicklas Nordborg |
3334 |
14 May 07 |
nicklas |
9 |
|
3334 |
14 May 07 |
nicklas |
This file is part of BASE - BioArray Software Environment. |
3334 |
14 May 07 |
nicklas |
Available at http://base.thep.lu.se/ |
3334 |
14 May 07 |
nicklas |
12 |
|
3334 |
14 May 07 |
nicklas |
BASE is free software; you can redistribute it and/or |
3334 |
14 May 07 |
nicklas |
modify it under the terms of the GNU General Public License |
4477 |
05 Sep 08 |
jari |
as published by the Free Software Foundation; either version 3 |
3334 |
14 May 07 |
nicklas |
of the License, or (at your option) any later version. |
3334 |
14 May 07 |
nicklas |
17 |
|
3334 |
14 May 07 |
nicklas |
BASE is distributed in the hope that it will be useful, |
3334 |
14 May 07 |
nicklas |
but WITHOUT ANY WARRANTY; without even the implied warranty of |
3334 |
14 May 07 |
nicklas |
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
3334 |
14 May 07 |
nicklas |
GNU General Public License for more details. |
3334 |
14 May 07 |
nicklas |
22 |
|
3334 |
14 May 07 |
nicklas |
You should have received a copy of the GNU General Public License |
4509 |
11 Sep 08 |
jari |
along with BASE. If not, see <http://www.gnu.org/licenses/>. |
3334 |
14 May 07 |
nicklas |
25 |
--> |
3334 |
14 May 07 |
nicklas |
26 |
|
3334 |
14 May 07 |
nicklas |
27 |
<appendix id="appendix.rawdatatypes"> |
5782 |
04 Oct 11 |
nicklas |
28 |
<?dbhtml filename="rawdatatypes.html" ?> |
3757 |
20 Sep 07 |
nicklas |
29 |
<title>Platforms and raw-data-types.xml reference</title> |
3757 |
20 Sep 07 |
nicklas |
30 |
|
3757 |
20 Sep 07 |
nicklas |
31 |
<para> |
4002 |
26 Nov 07 |
nicklas |
32 |
Raw data can be stored either as files attached to items and/or in |
4002 |
26 Nov 07 |
nicklas |
33 |
the database. The <classname docapi="net.sf.basedb.core">Platform</classname> |
4002 |
26 Nov 07 |
nicklas |
34 |
item has information about this. For more information see |
4002 |
26 Nov 07 |
nicklas |
35 |
<xref linkend="core_api.data_in_files" />. |
3757 |
20 Sep 07 |
nicklas |
36 |
</para> |
3757 |
20 Sep 07 |
nicklas |
37 |
|
3757 |
20 Sep 07 |
nicklas |
38 |
<sect1 id="appendix.rawdatatypes.platforms"> |
5678 |
29 Jun 11 |
nicklas |
39 |
<title>Default platforms and variants installed with BASE</title> |
3757 |
20 Sep 07 |
nicklas |
40 |
|
3757 |
20 Sep 07 |
nicklas |
41 |
<informaltable> |
3757 |
20 Sep 07 |
nicklas |
42 |
<tgroup cols="7"> |
3757 |
20 Sep 07 |
nicklas |
43 |
<colspec colname="platform.name" /> |
3757 |
20 Sep 07 |
nicklas |
44 |
<colspec colname="platform.id" /> |
3757 |
20 Sep 07 |
nicklas |
45 |
<colspec colname="variant.name" /> |
3757 |
20 Sep 07 |
nicklas |
46 |
<colspec colname="variant.id" /> |
3757 |
20 Sep 07 |
nicklas |
47 |
<colspec colname="filetype.item" /> |
3757 |
20 Sep 07 |
nicklas |
48 |
<colspec colname="filetype.name" /> |
3757 |
20 Sep 07 |
nicklas |
49 |
<colspec colname="filetype.id" /> |
3757 |
20 Sep 07 |
nicklas |
50 |
<thead> |
3757 |
20 Sep 07 |
nicklas |
51 |
<row> |
3757 |
20 Sep 07 |
nicklas |
52 |
<entry namest="platform.name" nameend="platform.id">Platform</entry> |
3757 |
20 Sep 07 |
nicklas |
53 |
<entry namest="variant.name" nameend="variant.id">Variants</entry> |
3835 |
15 Oct 07 |
nicklas |
54 |
<entry namest="filetype.item" nameend="filetype.id">Data file types</entry> |
3757 |
20 Sep 07 |
nicklas |
55 |
</row> |
3757 |
20 Sep 07 |
nicklas |
56 |
<row> |
3757 |
20 Sep 07 |
nicklas |
57 |
<entry>Name</entry> |
3757 |
20 Sep 07 |
nicklas |
58 |
<entry>ID</entry> |
3757 |
20 Sep 07 |
nicklas |
59 |
<entry>Name</entry> |
3757 |
20 Sep 07 |
nicklas |
60 |
<entry>ID</entry> |
3757 |
20 Sep 07 |
nicklas |
61 |
<entry>Item</entry> |
3757 |
20 Sep 07 |
nicklas |
62 |
<entry>Name</entry> |
3757 |
20 Sep 07 |
nicklas |
63 |
<entry>ID</entry> |
3757 |
20 Sep 07 |
nicklas |
64 |
</row> |
3757 |
20 Sep 07 |
nicklas |
65 |
</thead> |
3757 |
20 Sep 07 |
nicklas |
66 |
<tbody> |
3757 |
20 Sep 07 |
nicklas |
67 |
<row> |
3757 |
20 Sep 07 |
nicklas |
68 |
<entry morerows="2">Generic</entry> |
3757 |
20 Sep 07 |
nicklas |
69 |
<entry morerows="2">generic</entry> |
3835 |
15 Oct 07 |
nicklas |
70 |
<entry morerows="2">-</entry> |
3835 |
15 Oct 07 |
nicklas |
71 |
<entry morerows="2">-</entry> |
3334 |
14 May 07 |
nicklas |
72 |
|
3757 |
20 Sep 07 |
nicklas |
73 |
<entry morerows="1">Array design</entry> |
3757 |
20 Sep 07 |
nicklas |
74 |
<entry>Reporter map</entry> |
3757 |
20 Sep 07 |
nicklas |
75 |
<entry>generic.reportermap</entry> |
3757 |
20 Sep 07 |
nicklas |
76 |
</row> |
3757 |
20 Sep 07 |
nicklas |
77 |
<row> |
3757 |
20 Sep 07 |
nicklas |
78 |
<entry>Print map</entry> |
3757 |
20 Sep 07 |
nicklas |
79 |
<entry>generic.printmap</entry> |
3757 |
20 Sep 07 |
nicklas |
80 |
</row> |
3757 |
20 Sep 07 |
nicklas |
81 |
<row> |
3757 |
20 Sep 07 |
nicklas |
82 |
<entry>Raw bioassay</entry> |
3835 |
15 Oct 07 |
nicklas |
83 |
<entry>Generic raw data</entry> |
3757 |
20 Sep 07 |
nicklas |
84 |
<entry>generic.rawdata</entry> |
3757 |
20 Sep 07 |
nicklas |
85 |
</row> |
3757 |
20 Sep 07 |
nicklas |
86 |
<row> |
3835 |
15 Oct 07 |
nicklas |
87 |
<entry morerows="1">Affymetrix</entry> |
3835 |
15 Oct 07 |
nicklas |
88 |
<entry morerows="1">affymetrix</entry> |
3835 |
15 Oct 07 |
nicklas |
89 |
<entry morerows="1">-</entry> |
3835 |
15 Oct 07 |
nicklas |
90 |
<entry morerows="1">-</entry> |
3757 |
20 Sep 07 |
nicklas |
91 |
<entry>Array design</entry> |
3835 |
15 Oct 07 |
nicklas |
92 |
<entry>CDF file</entry> |
3757 |
20 Sep 07 |
nicklas |
93 |
<entry>affymetrix.cdf</entry> |
3757 |
20 Sep 07 |
nicklas |
94 |
</row> |
3757 |
20 Sep 07 |
nicklas |
95 |
<row> |
3757 |
20 Sep 07 |
nicklas |
96 |
<entry>Raw bioassay</entry> |
3835 |
15 Oct 07 |
nicklas |
97 |
<entry>CEL file</entry> |
3757 |
20 Sep 07 |
nicklas |
98 |
<entry>affymetrix.cel</entry> |
3757 |
20 Sep 07 |
nicklas |
99 |
</row> |
5780 |
04 Oct 11 |
nicklas |
100 |
<row> |
5780 |
04 Oct 11 |
nicklas |
101 |
<entry morerows="1">Sequencing</entry> |
5780 |
04 Oct 11 |
nicklas |
102 |
<entry morerows="1">sequencing</entry> |
5780 |
04 Oct 11 |
nicklas |
103 |
<entry morerows="1">Expression-like</entry> |
5780 |
04 Oct 11 |
nicklas |
104 |
<entry morerows="1">sequencing.expression</entry> |
5780 |
04 Oct 11 |
nicklas |
105 |
<entry>Array design</entry> |
5780 |
04 Oct 11 |
nicklas |
106 |
<entry>GTF ref-seq file</entry> |
5780 |
04 Oct 11 |
nicklas |
107 |
<entry>refseq.gtf</entry> |
5780 |
04 Oct 11 |
nicklas |
108 |
</row> |
5780 |
04 Oct 11 |
nicklas |
109 |
<row> |
5780 |
04 Oct 11 |
nicklas |
110 |
<entry>Raw bioassay</entry> |
5780 |
04 Oct 11 |
nicklas |
111 |
<entry>FPKM tracking file</entry> |
5780 |
04 Oct 11 |
nicklas |
112 |
<entry> sequencing.fpkm_tracking</entry> |
5780 |
04 Oct 11 |
nicklas |
113 |
</row> |
3757 |
20 Sep 07 |
nicklas |
114 |
</tbody> |
3757 |
20 Sep 07 |
nicklas |
115 |
</tgroup> |
3757 |
20 Sep 07 |
nicklas |
116 |
</informaltable> |
3757 |
20 Sep 07 |
nicklas |
117 |
|
3757 |
20 Sep 07 |
nicklas |
118 |
|
3757 |
20 Sep 07 |
nicklas |
119 |
</sect1> |
3757 |
20 Sep 07 |
nicklas |
120 |
|
3757 |
20 Sep 07 |
nicklas |
121 |
<sect1 id="appendix.rawdatatypes.ref"> |
3757 |
20 Sep 07 |
nicklas |
122 |
<title>raw-data-types.xml reference</title> |
3757 |
20 Sep 07 |
nicklas |
123 |
|
3757 |
20 Sep 07 |
nicklas |
124 |
<para> |
4002 |
26 Nov 07 |
nicklas |
125 |
A given platform either supports importing data to the database or it |
4002 |
26 Nov 07 |
nicklas |
126 |
doesn't. If it supports import, it may be locked to specific raw data type |
4002 |
26 Nov 07 |
nicklas |
127 |
or it may use any raw data type. Among the default platforms installed with |
4005 |
26 Nov 07 |
martin |
128 |
BASE, the Affymetrix platform doesn't support importing data while the Generic |
4005 |
26 Nov 07 |
martin |
129 |
platform supports importing to any raw data type. |
3757 |
20 Sep 07 |
nicklas |
130 |
</para> |
3757 |
20 Sep 07 |
nicklas |
131 |
|
4002 |
26 Nov 07 |
nicklas |
132 |
<para> |
4002 |
26 Nov 07 |
nicklas |
133 |
Raw data types are defined in the <filename>raw-data-types.xml</filename> |
4002 |
26 Nov 07 |
nicklas |
134 |
file. This file is located in the <filename><basedir>/www/WEB-INF/classes</filename> |
4002 |
26 Nov 07 |
nicklas |
135 |
directory and contains information about the database tables and columns to |
4002 |
26 Nov 07 |
nicklas |
136 |
use for storing raw data. BASE ships with default raw data types for many |
4002 |
26 Nov 07 |
nicklas |
137 |
different microarray platforms, including Genepix, Agilent and Illumina. |
4002 |
26 Nov 07 |
nicklas |
138 |
</para> |
4002 |
26 Nov 07 |
nicklas |
139 |
|
5678 |
29 Jun 11 |
nicklas |
140 |
<tip> |
5678 |
29 Jun 11 |
nicklas |
141 |
<para> |
5678 |
29 Jun 11 |
nicklas |
142 |
It is also possible to put additional raw data type definitions in the |
5678 |
29 Jun 11 |
nicklas |
143 |
<filename><basedir>/www/WEB-INF/classes/raw-data-types</filename> |
5678 |
29 Jun 11 |
nicklas |
144 |
subdirectory. BASE will merge all <filename>*.xml</filename> it finds with |
5678 |
29 Jun 11 |
nicklas |
145 |
the main <filename>raw-data-types.xml</filename> file. The extra |
5678 |
29 Jun 11 |
nicklas |
146 |
configuration files should have the same format as the main |
5678 |
29 Jun 11 |
nicklas |
147 |
<filename>raw-data-types.xml</filename> file. Duplicate raw data types |
5678 |
29 Jun 11 |
nicklas |
148 |
are not supported and it is not possible to add extra columns to |
5678 |
29 Jun 11 |
nicklas |
149 |
existing types using this approach. |
5678 |
29 Jun 11 |
nicklas |
150 |
</para> |
5678 |
29 Jun 11 |
nicklas |
151 |
</tip> |
5678 |
29 Jun 11 |
nicklas |
152 |
|
4002 |
26 Nov 07 |
nicklas |
153 |
<para> |
4002 |
26 Nov 07 |
nicklas |
154 |
If you want your BASE installation to be configured differently we recommend that |
4002 |
26 Nov 07 |
nicklas |
155 |
you do it before the first initialisation of the database. |
4002 |
26 Nov 07 |
nicklas |
156 |
It is possible to change the configuration of an existing BASE installation but it |
4005 |
26 Nov 07 |
martin |
157 |
requires manual updates to the database. Following procedure covers how to update: |
4002 |
26 Nov 07 |
nicklas |
158 |
</para> |
4002 |
26 Nov 07 |
nicklas |
159 |
|
4002 |
26 Nov 07 |
nicklas |
160 |
<orderedlist> |
4002 |
26 Nov 07 |
nicklas |
161 |
<listitem> |
4002 |
26 Nov 07 |
nicklas |
162 |
<para> |
4002 |
26 Nov 07 |
nicklas |
163 |
Shut down the BASE web server. If you have installed job agents you should shut |
4002 |
26 Nov 07 |
nicklas |
164 |
down them as well. |
4002 |
26 Nov 07 |
nicklas |
165 |
</para> |
4002 |
26 Nov 07 |
nicklas |
166 |
</listitem> |
4002 |
26 Nov 07 |
nicklas |
167 |
|
4002 |
26 Nov 07 |
nicklas |
168 |
<listitem> |
4002 |
26 Nov 07 |
nicklas |
169 |
<para> |
5678 |
29 Jun 11 |
nicklas |
170 |
Modify the <filename>raw-data-types.xml</filename> file or create a new file |
5678 |
29 Jun 11 |
nicklas |
171 |
in the <filename>raw-data-types</filename> subdirectory. If you have installed |
4002 |
26 Nov 07 |
nicklas |
172 |
job agents, make sure they all have the same version as the web server. |
4002 |
26 Nov 07 |
nicklas |
173 |
</para> |
4002 |
26 Nov 07 |
nicklas |
174 |
</listitem> |
4002 |
26 Nov 07 |
nicklas |
175 |
|
4002 |
26 Nov 07 |
nicklas |
176 |
<listitem> |
4002 |
26 Nov 07 |
nicklas |
177 |
<para> |
4002 |
26 Nov 07 |
nicklas |
178 |
Run the <filename>updatedb.sh</filename> script. Tables for new raw data types |
4002 |
26 Nov 07 |
nicklas |
179 |
and new columns for existing raw data types automatically be created, but the script |
4002 |
26 Nov 07 |
nicklas |
180 |
can't delete tables or columns that have been removed, or modify columns that have |
4002 |
26 Nov 07 |
nicklas |
181 |
changed datatype. You will have to do these kind of changes by manually executing |
4002 |
26 Nov 07 |
nicklas |
182 |
SQL against your database. Check your database documentation for information about SQL syntax. |
4002 |
26 Nov 07 |
nicklas |
183 |
</para> |
4002 |
26 Nov 07 |
nicklas |
184 |
|
4002 |
26 Nov 07 |
nicklas |
185 |
<tip> |
4005 |
26 Nov 07 |
martin |
186 |
<title>Create a parallel installation</title> |
4002 |
26 Nov 07 |
nicklas |
187 |
<para> |
4005 |
26 Nov 07 |
martin |
188 |
You can always create a new temporary parallel installation to check |
4002 |
26 Nov 07 |
nicklas |
189 |
what the table generated by installation script looks like. Compare the |
4002 |
26 Nov 07 |
nicklas |
190 |
new table to the existing one and make sure they match. |
4002 |
26 Nov 07 |
nicklas |
191 |
</para> |
4002 |
26 Nov 07 |
nicklas |
192 |
</tip> |
4002 |
26 Nov 07 |
nicklas |
193 |
</listitem> |
4002 |
26 Nov 07 |
nicklas |
194 |
|
4002 |
26 Nov 07 |
nicklas |
195 |
<listitem> |
4002 |
26 Nov 07 |
nicklas |
196 |
<para> |
4002 |
26 Nov 07 |
nicklas |
197 |
Start up the BASE web server and job agents, if any, again. |
4002 |
26 Nov 07 |
nicklas |
198 |
</para> |
4002 |
26 Nov 07 |
nicklas |
199 |
</listitem> |
4002 |
26 Nov 07 |
nicklas |
200 |
</orderedlist> |
4002 |
26 Nov 07 |
nicklas |
201 |
|
4002 |
26 Nov 07 |
nicklas |
202 |
<tip> |
4002 |
26 Nov 07 |
nicklas |
203 |
<title>Start with few columns</title> |
4002 |
26 Nov 07 |
nicklas |
204 |
<para> |
4002 |
26 Nov 07 |
nicklas |
205 |
It is better to start with too few columns, since it is easier to add |
4002 |
26 Nov 07 |
nicklas |
206 |
more columns than it is to remove columns that are not needed. |
4002 |
26 Nov 07 |
nicklas |
207 |
</para> |
4002 |
26 Nov 07 |
nicklas |
208 |
</tip> |
4002 |
26 Nov 07 |
nicklas |
209 |
|
4002 |
26 Nov 07 |
nicklas |
210 |
<bridgehead>Format of the raw-data-types.xml file</bridgehead> |
4002 |
26 Nov 07 |
nicklas |
211 |
<para> |
4005 |
26 Nov 07 |
martin |
212 |
The following example will serve as a description of the format used in |
4005 |
26 Nov 07 |
martin |
213 |
<filename>raw-data-types.xml</filename>: |
4002 |
26 Nov 07 |
nicklas |
214 |
</para> |
4005 |
26 Nov 07 |
martin |
215 |
|
4005 |
26 Nov 07 |
martin |
216 |
|
4002 |
26 Nov 07 |
nicklas |
217 |
<programlisting language="xml"> |
4002 |
26 Nov 07 |
nicklas |
218 |
<![CDATA[ |
4002 |
26 Nov 07 |
nicklas |
219 |
<?xml version="1.0" ?> |
4002 |
26 Nov 07 |
nicklas |
220 |
<?xml-stylesheet type="text/xsl" href="raw-data-types.xsl"?> |
4002 |
26 Nov 07 |
nicklas |
221 |
<!DOCTYPE raw-data-types SYSTEM "raw-data-types.dtd" > |
4002 |
26 Nov 07 |
nicklas |
222 |
<raw-data-types> |
4002 |
26 Nov 07 |
nicklas |
223 |
<raw-data-type |
4002 |
26 Nov 07 |
nicklas |
224 |
id="genepix" |
4002 |
26 Nov 07 |
nicklas |
225 |
name="GenePix" |
4002 |
26 Nov 07 |
nicklas |
226 |
channels="2" |
4002 |
26 Nov 07 |
nicklas |
227 |
table="RawDataGenePix" |
4002 |
26 Nov 07 |
nicklas |
228 |
> |
4002 |
26 Nov 07 |
nicklas |
229 |
<property |
4002 |
26 Nov 07 |
nicklas |
230 |
name="diameter" |
4002 |
26 Nov 07 |
nicklas |
231 |
title="Spot diameter" |
4002 |
26 Nov 07 |
nicklas |
232 |
description="The diameter of the spot in µm" |
4002 |
26 Nov 07 |
nicklas |
233 |
column="diameter" |
4002 |
26 Nov 07 |
nicklas |
234 |
type="float" |
4002 |
26 Nov 07 |
nicklas |
235 |
/> |
4002 |
26 Nov 07 |
nicklas |
236 |
<property |
4002 |
26 Nov 07 |
nicklas |
237 |
name="ch1FgMedian" |
4002 |
26 Nov 07 |
nicklas |
238 |
title="Channel 1 foreground median" |
4002 |
26 Nov 07 |
nicklas |
239 |
description="The median of the foreground intensity in channel 1" |
4002 |
26 Nov 07 |
nicklas |
240 |
column="ch1_fg_median" |
4002 |
26 Nov 07 |
nicklas |
241 |
type="float" |
4002 |
26 Nov 07 |
nicklas |
242 |
channel="1" |
4002 |
26 Nov 07 |
nicklas |
243 |
/> |
4002 |
26 Nov 07 |
nicklas |
<!-- skipped a lot of properties --> |
4002 |
26 Nov 07 |
nicklas |
245 |
<intensity-formula |
4002 |
26 Nov 07 |
nicklas |
246 |
name="mean" |
4002 |
26 Nov 07 |
nicklas |
247 |
title="Mean FG - Mean BG" |
4002 |
26 Nov 07 |
nicklas |
248 |
description="Subtract mean background from mean foreground" |
4002 |
26 Nov 07 |
nicklas |
249 |
> |
4002 |
26 Nov 07 |
nicklas |
250 |
<formula |
4002 |
26 Nov 07 |
nicklas |
251 |
channel="1" |
4002 |
26 Nov 07 |
nicklas |
252 |
expression="raw('ch1FgMean') - raw('ch1BgMean')" |
4002 |
26 Nov 07 |
nicklas |
253 |
/> |
4002 |
26 Nov 07 |
nicklas |
254 |
<formula |
4002 |
26 Nov 07 |
nicklas |
255 |
channel="2" |
4002 |
26 Nov 07 |
nicklas |
256 |
expression="raw('ch2FgMean') - raw('ch2BgMean')" |
4002 |
26 Nov 07 |
nicklas |
257 |
/> |
4002 |
26 Nov 07 |
nicklas |
258 |
</intensity-formula> |
4002 |
26 Nov 07 |
nicklas |
<!-- and a few more... ---> |
4002 |
26 Nov 07 |
nicklas |
260 |
</raw-data-type> |
4002 |
26 Nov 07 |
nicklas |
261 |
</raw-data-types> |
4002 |
26 Nov 07 |
nicklas |
262 |
]]> |
4002 |
26 Nov 07 |
nicklas |
263 |
</programlisting> |
4002 |
26 Nov 07 |
nicklas |
264 |
|
4002 |
26 Nov 07 |
nicklas |
265 |
<para> |
4002 |
26 Nov 07 |
nicklas |
266 |
Each raw data type is represented by a <sgmltag class="starttag">raw-data-type</sgmltag> |
4002 |
26 Nov 07 |
nicklas |
267 |
tag. The following attributes can be used: |
4002 |
26 Nov 07 |
nicklas |
268 |
</para> |
4002 |
26 Nov 07 |
nicklas |
269 |
|
4002 |
26 Nov 07 |
nicklas |
270 |
<table frame="all" id="appendix.rawdatatypes.tag"> |
4002 |
26 Nov 07 |
nicklas |
271 |
<title>Attributes for the <sgmltag class="starttag">raw-data-type</sgmltag> tag</title> |
4002 |
26 Nov 07 |
nicklas |
272 |
<tgroup cols="3" align="left"> |
4002 |
26 Nov 07 |
nicklas |
273 |
<colspec colname="attribute" align="left" /> |
4002 |
26 Nov 07 |
nicklas |
274 |
<colspec colname="required" /> |
4002 |
26 Nov 07 |
nicklas |
275 |
<colspec colname="comment" /> |
4002 |
26 Nov 07 |
nicklas |
276 |
<thead> |
4002 |
26 Nov 07 |
nicklas |
277 |
<row> |
4002 |
26 Nov 07 |
nicklas |
278 |
<entry>Attribute</entry> |
4002 |
26 Nov 07 |
nicklas |
279 |
<entry>Required</entry> |
4002 |
26 Nov 07 |
nicklas |
280 |
<entry>Comment</entry> |
4002 |
26 Nov 07 |
nicklas |
281 |
</row> |
4002 |
26 Nov 07 |
nicklas |
282 |
</thead> |
4002 |
26 Nov 07 |
nicklas |
283 |
<tbody> |
4002 |
26 Nov 07 |
nicklas |
284 |
<row> |
4002 |
26 Nov 07 |
nicklas |
285 |
<entry>id</entry> |
4002 |
26 Nov 07 |
nicklas |
286 |
<entry>yes</entry> |
4002 |
26 Nov 07 |
nicklas |
287 |
<entry> |
4002 |
26 Nov 07 |
nicklas |
288 |
A unique ID of the raw data type. It should contain only letters, |
4002 |
26 Nov 07 |
nicklas |
289 |
numbers and underscores and the first character must be a letter. |
4002 |
26 Nov 07 |
nicklas |
290 |
</entry> |
4002 |
26 Nov 07 |
nicklas |
291 |
</row> |
4002 |
26 Nov 07 |
nicklas |
292 |
<row> |
4002 |
26 Nov 07 |
nicklas |
293 |
<entry>name</entry> |
4002 |
26 Nov 07 |
nicklas |
294 |
<entry>yes</entry> |
4002 |
26 Nov 07 |
nicklas |
295 |
<entry> |
4002 |
26 Nov 07 |
nicklas |
296 |
A unique name of the raw data type. The name is usually used by client |
4005 |
26 Nov 07 |
martin |
297 |
applications for display. |
4002 |
26 Nov 07 |
nicklas |
298 |
</entry> |
4002 |
26 Nov 07 |
nicklas |
299 |
</row> |
4002 |
26 Nov 07 |
nicklas |
300 |
<row> |
4002 |
26 Nov 07 |
nicklas |
301 |
<entry>table</entry> |
4002 |
26 Nov 07 |
nicklas |
302 |
<entry>yes</entry> |
4002 |
26 Nov 07 |
nicklas |
303 |
<entry> |
4002 |
26 Nov 07 |
nicklas |
304 |
The name of the database table to store data in. The table name |
4002 |
26 Nov 07 |
nicklas |
305 |
must be unique and can only contain letters, |
4002 |
26 Nov 07 |
nicklas |
306 |
numbers and underscores. The first character must be a letter. |
4002 |
26 Nov 07 |
nicklas |
307 |
</entry> |
4002 |
26 Nov 07 |
nicklas |
308 |
</row> |
4002 |
26 Nov 07 |
nicklas |
309 |
<row> |
4002 |
26 Nov 07 |
nicklas |
310 |
<entry>channels</entry> |
4002 |
26 Nov 07 |
nicklas |
311 |
<entry>yes</entry> |
4002 |
26 Nov 07 |
nicklas |
312 |
<entry> |
4002 |
26 Nov 07 |
nicklas |
313 |
The number of channels used by this raw data type. It must be |
4002 |
26 Nov 07 |
nicklas |
314 |
a number > 0. |
4002 |
26 Nov 07 |
nicklas |
315 |
</entry> |
4002 |
26 Nov 07 |
nicklas |
316 |
</row> |
4002 |
26 Nov 07 |
nicklas |
317 |
<row> |
4002 |
26 Nov 07 |
nicklas |
318 |
<entry>description</entry> |
4002 |
26 Nov 07 |
nicklas |
319 |
<entry>no</entry> |
4002 |
26 Nov 07 |
nicklas |
320 |
<entry> |
4002 |
26 Nov 07 |
nicklas |
321 |
An optional (longer) description of the raw data type. |
4002 |
26 Nov 07 |
nicklas |
322 |
</entry> |
4002 |
26 Nov 07 |
nicklas |
323 |
</row> |
4002 |
26 Nov 07 |
nicklas |
324 |
</tbody> |
4002 |
26 Nov 07 |
nicklas |
325 |
</tgroup> |
4002 |
26 Nov 07 |
nicklas |
326 |
</table> |
4002 |
26 Nov 07 |
nicklas |
327 |
|
4002 |
26 Nov 07 |
nicklas |
328 |
<para> |
4002 |
26 Nov 07 |
nicklas |
329 |
Following the <sgmltag class="starttag">raw-data-type</sgmltag> tag |
4002 |
26 Nov 07 |
nicklas |
330 |
is one or more <sgmltag class="starttag">property</sgmltag> tags. |
4002 |
26 Nov 07 |
nicklas |
331 |
Each one defines a column in the database that is designed to hold |
4002 |
26 Nov 07 |
nicklas |
332 |
data values of a particular type. The following attributes can be used |
4002 |
26 Nov 07 |
nicklas |
333 |
on this tag: |
4002 |
26 Nov 07 |
nicklas |
334 |
</para> |
4002 |
26 Nov 07 |
nicklas |
335 |
|
4002 |
26 Nov 07 |
nicklas |
336 |
<table frame="all" id="appendix.rawdatatypes.property"> |
4002 |
26 Nov 07 |
nicklas |
337 |
<title>Attributes for the <sgmltag class="starttag">property</sgmltag> tag</title> |
4002 |
26 Nov 07 |
nicklas |
338 |
<tgroup cols="3" align="left"> |
4002 |
26 Nov 07 |
nicklas |
339 |
<colspec colname="attribute" align="left" /> |
4002 |
26 Nov 07 |
nicklas |
340 |
<colspec colname="required" /> |
4002 |
26 Nov 07 |
nicklas |
341 |
<colspec colname="comment" /> |
4002 |
26 Nov 07 |
nicklas |
342 |
<thead> |
4002 |
26 Nov 07 |
nicklas |
343 |
<row> |
4002 |
26 Nov 07 |
nicklas |
344 |
<entry>Attribute</entry> |
4002 |
26 Nov 07 |
nicklas |
345 |
<entry>Required</entry> |
4002 |
26 Nov 07 |
nicklas |
346 |
<entry>Comment</entry> |
4002 |
26 Nov 07 |
nicklas |
347 |
</row> |
4002 |
26 Nov 07 |
nicklas |
348 |
</thead> |
4002 |
26 Nov 07 |
nicklas |
349 |
<tbody> |
4002 |
26 Nov 07 |
nicklas |
350 |
<row> |
4002 |
26 Nov 07 |
nicklas |
351 |
<entry>*</entry> |
4002 |
26 Nov 07 |
nicklas |
352 |
<entry></entry> |
4002 |
26 Nov 07 |
nicklas |
353 |
<entry> |
4002 |
26 Nov 07 |
nicklas |
354 |
All attributes defined by the |
4002 |
26 Nov 07 |
nicklas |
355 |
<sgmltag class="starttag">property</sgmltag> tag in |
4002 |
26 Nov 07 |
nicklas |
356 |
<filename>extended-properties.xml</filename>. See |
4002 |
26 Nov 07 |
nicklas |
357 |
<xref linkend="appendix.extendedproperties.property" />. |
4002 |
26 Nov 07 |
nicklas |
358 |
</entry> |
4002 |
26 Nov 07 |
nicklas |
359 |
</row> |
4002 |
26 Nov 07 |
nicklas |
360 |
<row> |
4002 |
26 Nov 07 |
nicklas |
361 |
<entry>channels</entry> |
4002 |
26 Nov 07 |
nicklas |
362 |
<entry>no</entry> |
4002 |
26 Nov 07 |
nicklas |
363 |
<entry> |
4002 |
26 Nov 07 |
nicklas |
364 |
The channel number the property belongs to. Allowed values are 0 to |
4002 |
26 Nov 07 |
nicklas |
365 |
the number of channels specified for the raw data type. If the property |
4002 |
26 Nov 07 |
nicklas |
366 |
doesn't belong to any channels set the value to 0 or leave it |
4002 |
26 Nov 07 |
nicklas |
367 |
unspecified. |
4002 |
26 Nov 07 |
nicklas |
368 |
</entry> |
4002 |
26 Nov 07 |
nicklas |
369 |
</row> |
4002 |
26 Nov 07 |
nicklas |
370 |
</tbody> |
4002 |
26 Nov 07 |
nicklas |
371 |
</tgroup> |
4002 |
26 Nov 07 |
nicklas |
372 |
</table> |
4002 |
26 Nov 07 |
nicklas |
373 |
|
4002 |
26 Nov 07 |
nicklas |
374 |
<para> |
4002 |
26 Nov 07 |
nicklas |
375 |
Following the <sgmltag class="starttag">property</sgmltag> tags comes 0 |
4002 |
26 Nov 07 |
nicklas |
376 |
or more <sgmltag class="starttag">intensity-formula</sgmltag> tags. |
4005 |
26 Nov 07 |
martin |
377 |
Each one defines mathematical formulas that can be used to |
4005 |
26 Nov 07 |
martin |
378 |
calculate the intensity values from the raw data. In the Genepix case, |
4002 |
26 Nov 07 |
nicklas |
379 |
there are several formulas which differs in the way background is |
4005 |
26 Nov 07 |
martin |
380 |
subtracted from foreground intensity values. For other raw data |
4002 |
26 Nov 07 |
nicklas |
381 |
types, the intensity formula may just copy one of the raw data values. |
4002 |
26 Nov 07 |
nicklas |
382 |
</para> |
4002 |
26 Nov 07 |
nicklas |
383 |
|
4002 |
26 Nov 07 |
nicklas |
384 |
<para> |
4002 |
26 Nov 07 |
nicklas |
385 |
The intensity formulas are installed as <classname |
4002 |
26 Nov 07 |
nicklas |
386 |
docapi="net.sf.basedb.core">Formula</classname> items in the database. This |
4002 |
26 Nov 07 |
nicklas |
387 |
means that you can manually add, change or remove intensity formulas directly |
4002 |
26 Nov 07 |
nicklas |
388 |
from the web interface. The intensity formulas in the <filename>raw-data-types.xml</filename> |
4002 |
26 Nov 07 |
nicklas |
389 |
file are only used at installation time. |
4002 |
26 Nov 07 |
nicklas |
390 |
</para> |
4002 |
26 Nov 07 |
nicklas |
391 |
|
4002 |
26 Nov 07 |
nicklas |
392 |
<para> |
4002 |
26 Nov 07 |
nicklas |
393 |
The <sgmltag class="starttag">intensity-formula</sgmltag> tag has the following |
4002 |
26 Nov 07 |
nicklas |
394 |
attributes: |
4002 |
26 Nov 07 |
nicklas |
395 |
</para> |
4002 |
26 Nov 07 |
nicklas |
396 |
|
4002 |
26 Nov 07 |
nicklas |
397 |
<table frame="all" id="appendix.rawdatatypes.intensity-formula"> |
4002 |
26 Nov 07 |
nicklas |
398 |
<title>Attributes for the <sgmltag class="starttag">intensity-formula</sgmltag> tag</title> |
4002 |
26 Nov 07 |
nicklas |
399 |
<tgroup cols="3" align="left"> |
4002 |
26 Nov 07 |
nicklas |
400 |
<colspec colname="attribute" align="left" /> |
4002 |
26 Nov 07 |
nicklas |
401 |
<colspec colname="required" /> |
4002 |
26 Nov 07 |
nicklas |
402 |
<colspec colname="comment" /> |
4002 |
26 Nov 07 |
nicklas |
403 |
<thead> |
4002 |
26 Nov 07 |
nicklas |
404 |
<row> |
4002 |
26 Nov 07 |
nicklas |
405 |
<entry>Attribute</entry> |
4002 |
26 Nov 07 |
nicklas |
406 |
<entry>Required</entry> |
4002 |
26 Nov 07 |
nicklas |
407 |
<entry>Comment</entry> |
4002 |
26 Nov 07 |
nicklas |
408 |
</row> |
4002 |
26 Nov 07 |
nicklas |
409 |
</thead> |
4002 |
26 Nov 07 |
nicklas |
410 |
<tbody> |
4002 |
26 Nov 07 |
nicklas |
411 |
<row> |
4002 |
26 Nov 07 |
nicklas |
412 |
<entry>name</entry> |
4002 |
26 Nov 07 |
nicklas |
413 |
<entry>yes</entry> |
4002 |
26 Nov 07 |
nicklas |
414 |
<entry> |
4002 |
26 Nov 07 |
nicklas |
415 |
A unique name for the formula. This is only used during installation. |
4002 |
26 Nov 07 |
nicklas |
416 |
</entry> |
4002 |
26 Nov 07 |
nicklas |
417 |
</row> |
4002 |
26 Nov 07 |
nicklas |
418 |
<row> |
4002 |
26 Nov 07 |
nicklas |
419 |
<entry>title</entry> |
4002 |
26 Nov 07 |
nicklas |
420 |
<entry>yes</entry> |
4002 |
26 Nov 07 |
nicklas |
421 |
<entry> |
4002 |
26 Nov 07 |
nicklas |
422 |
The title of the formula. This is used by client applications for |
4002 |
26 Nov 07 |
nicklas |
423 |
display. |
4002 |
26 Nov 07 |
nicklas |
424 |
</entry> |
4002 |
26 Nov 07 |
nicklas |
425 |
</row> |
4002 |
26 Nov 07 |
nicklas |
426 |
<row> |
4002 |
26 Nov 07 |
nicklas |
427 |
<entry>description</entry> |
4002 |
26 Nov 07 |
nicklas |
428 |
<entry>no</entry> |
4002 |
26 Nov 07 |
nicklas |
429 |
<entry> |
4002 |
26 Nov 07 |
nicklas |
430 |
An optional, longer, description of the formula. |
4002 |
26 Nov 07 |
nicklas |
431 |
</entry> |
4002 |
26 Nov 07 |
nicklas |
432 |
</row> |
4002 |
26 Nov 07 |
nicklas |
433 |
</tbody> |
4002 |
26 Nov 07 |
nicklas |
434 |
</tgroup> |
4002 |
26 Nov 07 |
nicklas |
435 |
</table> |
4002 |
26 Nov 07 |
nicklas |
436 |
|
4002 |
26 Nov 07 |
nicklas |
437 |
<para> |
4002 |
26 Nov 07 |
nicklas |
438 |
The <sgmltag class="starttag">intensity-formula</sgmltag> must contain |
4002 |
26 Nov 07 |
nicklas |
439 |
one <sgmltag class="starttag">formula</sgmltag> tag for each channel |
4002 |
26 Nov 07 |
nicklas |
440 |
of the raw data type. The attributes of this tag are: |
4002 |
26 Nov 07 |
nicklas |
441 |
</para> |
4002 |
26 Nov 07 |
nicklas |
442 |
|
4002 |
26 Nov 07 |
nicklas |
443 |
<table frame="all" id="appendix.rawdatatypes.formula"> |
4002 |
26 Nov 07 |
nicklas |
444 |
<title>Attributes for the <sgmltag class="starttag">formula</sgmltag> tag</title> |
4002 |
26 Nov 07 |
nicklas |
445 |
<tgroup cols="3" align="left"> |
4002 |
26 Nov 07 |
nicklas |
446 |
<colspec colname="attribute" align="left" /> |
4002 |
26 Nov 07 |
nicklas |
447 |
<colspec colname="required" /> |
4002 |
26 Nov 07 |
nicklas |
448 |
<colspec colname="comment" /> |
4002 |
26 Nov 07 |
nicklas |
449 |
<thead> |
4002 |
26 Nov 07 |
nicklas |
450 |
<row> |
4002 |
26 Nov 07 |
nicklas |
451 |
<entry>Attribute</entry> |
4002 |
26 Nov 07 |
nicklas |
452 |
<entry>Required</entry> |
4002 |
26 Nov 07 |
nicklas |
453 |
<entry>Comment</entry> |
4002 |
26 Nov 07 |
nicklas |
454 |
</row> |
4002 |
26 Nov 07 |
nicklas |
455 |
</thead> |
4002 |
26 Nov 07 |
nicklas |
456 |
<tbody> |
4002 |
26 Nov 07 |
nicklas |
457 |
<row> |
4002 |
26 Nov 07 |
nicklas |
458 |
<entry>channel</entry> |
4002 |
26 Nov 07 |
nicklas |
459 |
<entry>yes</entry> |
4002 |
26 Nov 07 |
nicklas |
460 |
<entry> |
4002 |
26 Nov 07 |
nicklas |
461 |
The channel number. One tag for each channel must be specified. No |
4002 |
26 Nov 07 |
nicklas |
462 |
duplicates are allowed. |
4002 |
26 Nov 07 |
nicklas |
463 |
</entry> |
4002 |
26 Nov 07 |
nicklas |
464 |
</row> |
4002 |
26 Nov 07 |
nicklas |
465 |
<row> |
4002 |
26 Nov 07 |
nicklas |
466 |
<entry>expression</entry> |
4002 |
26 Nov 07 |
nicklas |
467 |
<entry>yes</entry> |
4002 |
26 Nov 07 |
nicklas |
468 |
<entry> |
4002 |
26 Nov 07 |
nicklas |
469 |
The mathematical expression used to calculate the intensities. |
4002 |
26 Nov 07 |
nicklas |
470 |
The expression is parsed with the <classname docapi="net.sf.basedb.util.jep">Jep</classname> |
4002 |
26 Nov 07 |
nicklas |
471 |
parser. It supports the common mathematical operations such as +, -, *, /, |
4002 |
26 Nov 07 |
nicklas |
472 |
some mathematical function like, log2(), ln(), sqrt(), etc. See the API |
4002 |
26 Nov 07 |
nicklas |
473 |
documentation for Jep for more information. You can also use two special |
4002 |
26 Nov 07 |
nicklas |
474 |
function developed specifically for this case: |
4002 |
26 Nov 07 |
nicklas |
475 |
<itemizedlist> |
4002 |
26 Nov 07 |
nicklas |
476 |
<listitem> |
4002 |
26 Nov 07 |
nicklas |
477 |
<para> |
4002 |
26 Nov 07 |
nicklas |
478 |
raw(name): Get the value from the raw data property with the given name, |
4002 |
26 Nov 07 |
nicklas |
479 |
for example: <code>raw('ch1FgMedian')</code>. |
4002 |
26 Nov 07 |
nicklas |
480 |
</para> |
4002 |
26 Nov 07 |
nicklas |
481 |
</listitem> |
4002 |
26 Nov 07 |
nicklas |
482 |
<listitem> |
4002 |
26 Nov 07 |
nicklas |
483 |
<para> |
4002 |
26 Nov 07 |
nicklas |
484 |
mean(name): Get the mean value of the raw data property with the given name, |
4002 |
26 Nov 07 |
nicklas |
485 |
for example: <code>mean('ch1BgMean')</code>. The mean is calculated from |
4002 |
26 Nov 07 |
nicklas |
486 |
all raw data spots in the raw bioassay. |
4002 |
26 Nov 07 |
nicklas |
487 |
</para> |
4002 |
26 Nov 07 |
nicklas |
488 |
</listitem> |
4002 |
26 Nov 07 |
nicklas |
489 |
</itemizedlist> |
4002 |
26 Nov 07 |
nicklas |
490 |
</entry> |
4002 |
26 Nov 07 |
nicklas |
491 |
</row> |
4002 |
26 Nov 07 |
nicklas |
492 |
</tbody> |
4002 |
26 Nov 07 |
nicklas |
493 |
</tgroup> |
4002 |
26 Nov 07 |
nicklas |
494 |
</table> |
4002 |
26 Nov 07 |
nicklas |
495 |
|
3757 |
20 Sep 07 |
nicklas |
496 |
</sect1> |
3757 |
20 Sep 07 |
nicklas |
497 |
|
3334 |
14 May 07 |
nicklas |
498 |
</appendix> |
3334 |
14 May 07 |
nicklas |
499 |
|