source: trunk/doc/src/docbook/userdoc/experiments.xml @ 5682

Last change on this file since 5682 was 5682, checked in by Nicklas Nordborg, 10 years ago

References #1590: Documentation cleanup

FAQ section and removed information related to the Tab2Mage exporter.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Id Date
File size: 8.8 KB
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1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE sect1 PUBLIC
3    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
5<!--
6  $Id: experiments.xml 5682 2011-08-02 07:09:56Z nicklas $
7
8  Copyright (C) 2007 Jari Häkkinen, Peter Johansson, Nicklas Nordborg, Martin Svensson
9
10  This file is part of BASE - BioArray Software Environment.
11  Available at http://base.thep.lu.se/
12
13  BASE is free software; you can redistribute it and/or
14  modify it under the terms of the GNU General Public License
15  as published by the Free Software Foundation; either version 3
16  of the License, or (at your option) any later version.
17
18  BASE is distributed in the hope that it will be useful,
19  but WITHOUT ANY WARRANTY; without even the implied warranty of
20  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
21  GNU General Public License for more details.
22
23  You should have received a copy of the GNU General Public License
24  along with BASE. If not, see <http://www.gnu.org/licenses/>.
25-->
26
27<sect1 id="experiments_analysis.experiments">
28  <title>Experiments</title>
29  <para>
30    Experiments are the starting point for analysis. When you have
31    uploaded and imported your raw data, collected and registered all
32    information and annotations about samples, hybridizations, and other
33    items, it is time to collect everything in an experiment.
34  </para>
35 
36  <para>
37    To create a new experiment you can either mark one ore more
38    raw biossays on the raw bioassays list view and use the
39    <guibutton>New experiment</guibutton> button. You can also
40    create a new experiment from the experiments list view.
41  </para>
42
43  <sect2 id="experiments_analysis.experiment.properties">
44    <title>Experiment properties</title>
45   
46    <figure id="experiments_analysis.figures.experiment_properties">
47      <title>Create experiment</title>
48      <screenshot>
49        <mediaobject>
50          <imageobject><imagedata 
51            fileref="figures/experiment_properties.png" format="PNG"
52            /></imageobject>
53        </mediaobject>
54      </screenshot>
55    </figure>         
56   
57   
58    <helptext external_id="experiment.edit" title="Edit experiment">
59   
60      <variablelist>
61      <varlistentry>
62        <term><guilabel>Name</guilabel></term>
63        <listitem>
64          <para>
65            The name of the experiment.
66          </para>
67        </listitem>
68      </varlistentry>
69     
70      <varlistentry>
71        <term><guilabel>Raw data type</guilabel></term>
72        <listitem>
73          <para>
74            The raw data type to use in the experiment. All raw bioassays
75            must have raw data with this type.
76          </para>
77        </listitem>
78      </varlistentry>
79
80      <varlistentry>
81        <term><guilabel>Directory</guilabel></term>
82        <listitem>
83          <para>
84            A directory in the BASE file system where plug-ins
85            can save files that are generated during the analysis.
86            This is optional and if not given the plug-ins must ask
87            about a directory each time they need it. Use the
88            <guibutton>Select</guibutton> button to browse the file system
89            or create a new directory.
90          </para>
91        </listitem>
92      </varlistentry>
93     
94      <varlistentry>
95        <term><guilabel>Raw bioassays</guilabel></term>
96        <listitem>
97          <para>
98            The raw bioassays you want to analyze in this experiment. If
99            you created the experiment from the raw bioassays list the
100            selected raw bioassays are already filled in. Use the
101            <guibutton>Add raw bioassays</guibutton> button to add more
102            raw bioassays or the &gbRemove; button
103            to remove the selected raw bioassays from the list.
104          </para>
105        </listitem>
106      </varlistentry>
107     
108      <varlistentry>
109        <term><guilabel>Description</guilabel></term>
110        <listitem>
111          <para>
112            A description of the experiment.
113          </para>
114        </listitem>
115      </varlistentry>
116
117      </variablelist>
118     
119      <para>
120        Click on the &gbSave; button to save the
121        changes or on &gbCancel; to abort.
122      </para>
123     
124      <seeother>
125        <other external_id="experiment.edit.publication">Publication</other>
126        <other external_id="experiment.edit.factors">Experimental factors</other>
127      </seeother>
128    </helptext>
129   
130    <sect3 id="experiments_analysis.experiment.publication">
131      <title>The publication tab</title>
132     
133      <helptext external_id="experiment.edit.publication" 
134        title="Experiment publication">
135
136        <para>
137          On this tab you can enter information about a publication
138          that is the result of the experiment. All of this information
139          is optional.
140        </para>
141       
142        <variablelist>
143        <varlistentry>
144          <term><guilabel>PubMedId</guilabel></term>
145          <listitem>
146            <para>
147              The ID of the publication in the
148              <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query/static/overview.html"
149                >PubMed</ulink> database.
150            </para>
151          </listitem>
152        </varlistentry>
153        <varlistentry>
154          <term><guilabel>Title</guilabel></term>
155          <listitem>
156            <para>
157              The title of the publication.
158            </para>
159          </listitem>
160        </varlistentry>
161        <varlistentry>
162          <term><guilabel>Publication date</guilabel></term>
163          <listitem>
164            <para>
165              The date the article was published. Use the
166              <guibutton>Calendar</guibutton> button to select
167              a date from a pop-up window.
168            </para>
169          </listitem>
170        </varlistentry>
171        <varlistentry>
172          <term><guilabel>Abstract</guilabel></term>
173          <listitem>
174            <para>
175              The article abstract.
176            </para>
177          </listitem>
178        </varlistentry>
179        <varlistentry>
180          <term><guilabel>Experiment design</guilabel></term>
181          <listitem>
182            <para>
183              An explanation of the experiment design.
184            </para>
185          </listitem>
186        </varlistentry>
187        <varlistentry>
188          <term><guilabel>Experiment type</guilabel></term>
189          <listitem>
190            <para>
191              A description of the experiment type.
192            </para>
193          </listitem>
194        </varlistentry>
195        <varlistentry>
196          <term><guilabel>Affiliations</guilabel></term>
197          <listitem>
198            <para>
199              Partners and other related organisations that
200              have helped with the experiment.
201            </para>
202          </listitem>
203        </varlistentry>
204        <varlistentry>
205          <term><guilabel>Authors</guilabel></term>
206          <listitem>
207            <para>
208              The list of authors of the publication.
209            </para>
210          </listitem>
211        </varlistentry>
212        <varlistentry>
213          <term><guilabel>Publication</guilabel></term>
214          <listitem>
215            <para>
216              The body text of the publication.
217            </para>
218          </listitem>
219        </varlistentry>
220        </variablelist>
221       
222        <para>
223          Click on the &gbSave; button to save the
224          changes or on &gbCancel; to abort.
225        </para>
226     
227        <seeother>
228          <other external_id="experiment.edit">Experiment properties</other>
229          <other external_id="experiment.edit.factors">Experimental factors</other>
230        </seeother>
231      </helptext>
232    </sect3>
233   
234  </sect2>
235 
236  <sect2 id="experiments_analysis.experiment.factors">
237    <title>Experimental factors</title>
238   
239    <helptext external_id="experiment.edit.factors" 
240      title="Experimental factors">
241   
242      <para>
243        The experimental factors of an experiment are the variables
244        you are studying in the experiment. Typically the value of
245        an experimental factor is varied between samples or group of samples.
246        Different treatment methods is an example of an experimental factor.
247      </para>
248     
249      <para>
250        In the BASE world an experimental factor is the same as an annotation
251        type. Since you probably have lots of annotations on your items that are not
252        relevant for the experiment you must select the annotations types
253        that should make up the experimental factors of the experiment.
254      </para>
255     
256      <para>
257        Use the <guibutton>Add annotation types</guibutton> button to
258        select the annotation types that should be used as experimental
259        factors. The &gbRemove; button removes the
260        selected annotation types.
261      </para>
262
263      <para>
264        Click on the &gbSave; button to save the
265        changes or on &gbCancel; to abort.
266      </para>
267     
268      <para>
269        To be able to use the values of the experimental factors
270        in the analysis of your data the values must be accessible
271        from the raw bioassays. Since most of your annotations are
272        probably made at the sample or biosource level the raw bioassays
273        must inherit those annotations.
274        <nohelp>Read <xref linkend="annotations.inheriting" /> 
275        for more information about this.</nohelp>
276      </para>
277     
278      <tip>
279        <para>
280        Use the <guilabel>Item overview</guilabel> function to
281        verify that all your raw bioassays has been annotated or
282        inherited values for all experimental factors. If not, you
283        should do that before starting with the analysis.
284        </para>
285      </tip>
286     
287      <seeother>
288        <other external_id="experiment.edit">Experiment properties</other>
289        <other external_id="experiment.edit.publication">Publication</other>
290        <other external_id="item.overview">Item overview</other>
291        <other external_id="annotations.edit.inerited">Inherit annotations</other>
292      </seeother>
293     
294    </helptext>
295  </sect2>
296
297</sect1>
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