source: trunk/doc/src/docbook/user/experiments.xml @ 5783

Last change on this file since 5783 was 5783, checked in by Nicklas Nordborg, 10 years ago

References #1590: Documentation cleanup

Experiments and analysis chapter.

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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 5783 2011-10-05 10:34:24Z 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  <?dbhtml filename="experiments.html" ?>
29  <title>Experiments</title>
30  <para>
31    Experiments are the starting point for analysis. When you have
32    uploaded and imported your raw data, collected and registered all
33    information and annotations about samples, bioassays, and other
34    items, it is time to collect everything in an experiment.
35  </para>
36 
37  <para>
38    To create a new experiment you can either mark one ore more
39    raw biossays on the raw bioassays list view and use the
40    <guibutton>New experiment</guibutton> button. You can also
41    create a new experiment from the experiments list view.
42  </para>
43
44  <sect2 id="experiments_analysis.experiment.properties">
45    <title>Experiment properties</title>
46   
47    <figure id="experiments_analysis.figures.experiment_properties">
48      <title>Create experiment</title>
49      <screenshot>
50        <mediaobject>
51          <imageobject><imagedata 
52            fileref="figures/experiment_properties.png" format="PNG"
53            /></imageobject>
54        </mediaobject>
55      </screenshot>
56    </figure>         
57   
58   
59    <helptext external_id="experiment.edit" title="Edit experiment">
60   
61      <variablelist>
62      <varlistentry>
63        <term><guilabel>Name</guilabel></term>
64        <listitem>
65          <para>
66            The name of the experiment.
67          </para>
68        </listitem>
69      </varlistentry>
70     
71      <varlistentry>
72        <term><guilabel>Raw data type</guilabel></term>
73        <listitem>
74          <para>
75            The raw data type to use in the experiment. All raw bioassays
76            must have raw data with this type.
77          </para>
78        </listitem>
79      </varlistentry>
80
81      <varlistentry>
82        <term><guilabel>Directory</guilabel></term>
83        <listitem>
84          <para>
85            A directory in the BASE file system where plug-ins
86            can save files that are generated during the analysis.
87            This is optional and if not given the plug-ins must ask
88            about a directory each time they need it. Use the
89            <guibutton>Select</guibutton> button to browse the file system
90            or create a new directory.
91          </para>
92        </listitem>
93      </varlistentry>
94     
95      <varlistentry>
96        <term><guilabel>Raw bioassays</guilabel></term>
97        <listitem>
98          <para>
99            The raw bioassays you want to analyze in this experiment. If
100            you created the experiment from the raw bioassays list the
101            selected raw bioassays are already filled in. Use the
102            <guibutton>Add raw bioassays</guibutton> button to add more
103            raw bioassays or the &gbRemove; button
104            to remove the selected raw bioassays from the list.
105          </para>
106        </listitem>
107      </varlistentry>
108     
109      <varlistentry>
110        <term><guilabel>Description</guilabel></term>
111        <listitem>
112          <para>
113            A description of the experiment.
114          </para>
115        </listitem>
116      </varlistentry>
117
118      </variablelist>
119     
120      <para>
121        Click on the &gbSave; button to save the
122        changes or on &gbCancel; to abort.
123      </para>
124     
125      <seeother>
126        <other external_id="experiment.edit.publication">Publication</other>
127        <other external_id="experiment.edit.factors">Experimental factors</other>
128      </seeother>
129    </helptext>
130   
131    <sect3 id="experiments_analysis.experiment.publication">
132      <title>The publication tab</title>
133     
134      <helptext external_id="experiment.edit.publication" 
135        title="Experiment publication">
136
137        <para>
138          On this tab you can enter information about a publication
139          that is the result of the experiment. All of this information
140          is optional.
141        </para>
142       
143        <variablelist>
144        <varlistentry>
145          <term><guilabel>PubMedId</guilabel></term>
146          <listitem>
147            <para>
148              The ID of the publication in the
149              <ulink url="http://www.ncbi.nlm.nih.gov/pubmed/"
150                >PubMed</ulink> database.
151            </para>
152          </listitem>
153        </varlistentry>
154        <varlistentry>
155          <term><guilabel>Title</guilabel></term>
156          <listitem>
157            <para>
158              The title of the publication.
159            </para>
160          </listitem>
161        </varlistentry>
162        <varlistentry>
163          <term><guilabel>Publication date</guilabel></term>
164          <listitem>
165            <para>
166              The date the article was published. Use the
167              <guibutton>Calendar</guibutton> button to select
168              a date from a pop-up window.
169            </para>
170          </listitem>
171        </varlistentry>
172        <varlistentry>
173          <term><guilabel>Abstract</guilabel></term>
174          <listitem>
175            <para>
176              The article abstract.
177            </para>
178          </listitem>
179        </varlistentry>
180        <varlistentry>
181          <term><guilabel>Experiment design</guilabel></term>
182          <listitem>
183            <para>
184              An explanation of the experiment design.
185            </para>
186          </listitem>
187        </varlistentry>
188        <varlistentry>
189          <term><guilabel>Experiment type</guilabel></term>
190          <listitem>
191            <para>
192              A description of the experiment type.
193            </para>
194          </listitem>
195        </varlistentry>
196        <varlistentry>
197          <term><guilabel>Affiliations</guilabel></term>
198          <listitem>
199            <para>
200              Partners and other related organisations that
201              have helped with the experiment.
202            </para>
203          </listitem>
204        </varlistentry>
205        <varlistentry>
206          <term><guilabel>Authors</guilabel></term>
207          <listitem>
208            <para>
209              The list of authors of the publication.
210            </para>
211          </listitem>
212        </varlistentry>
213        <varlistentry>
214          <term><guilabel>Publication</guilabel></term>
215          <listitem>
216            <para>
217              The body text of the publication.
218            </para>
219          </listitem>
220        </varlistentry>
221        </variablelist>
222       
223        <para>
224          Click on the &gbSave; button to save the
225          changes or on &gbCancel; to abort.
226        </para>
227     
228        <seeother>
229          <other external_id="experiment.edit">Experiment properties</other>
230          <other external_id="experiment.edit.factors">Experimental factors</other>
231        </seeother>
232      </helptext>
233    </sect3>
234   
235  </sect2>
236 
237  <sect2 id="experiments_analysis.experiment.factors">
238    <title>Experimental factors</title>
239   
240    <helptext external_id="experiment.edit.factors" 
241      title="Experimental factors">
242   
243      <para>
244        The experimental factors of an experiment are the variables
245        you are studying in the experiment. Typically the value of
246        an experimental factor is varied between samples or group of samples.
247        Different treatment methods is an example of an experimental factor.
248      </para>
249     
250      <para>
251        In the BASE world an experimental factor is the same as an annotation
252        type. Since you probably have lots of annotations on your items that are not
253        relevant for the experiment you must select the annotations types
254        that should make up the experimental factors of the experiment.
255      </para>
256     
257      <para>
258        Use the <guibutton>Add annotation types</guibutton> button to
259        select the annotation types that should be used as experimental
260        factors. The &gbRemove; button removes the
261        selected annotation types.
262      </para>
263
264      <para>
265        Click on the &gbSave; button to save the
266        changes or on &gbCancel; to abort.
267      </para>
268     
269      <para>
270        To be able to use the values of the experimental factors
271        in the analysis of your data the values must be accessible
272        from the raw bioassays. Since most of your annotations are
273        probably made at the sample or biosource level the raw bioassays
274        must inherit those annotations.
275        <nohelp>Read <xref linkend="annotations.inheriting" /> 
276        for more information about this.</nohelp>
277      </para>
278     
279      <tip>
280        <para>
281        Use the <guilabel>Item overview</guilabel> function to
282        verify that all your raw bioassays has been annotated or
283        inherited values for all experimental factors. If not, you
284        should do that before starting with the analysis.
285        </para>
286      </tip>
287     
288      <seeother>
289        <other external_id="experiment.edit">Experiment properties</other>
290        <other external_id="experiment.edit.publication">Publication</other>
291        <other external_id="item.overview">Item overview</other>
292        <other external_id="annotations.edit.inerited">Inherit annotations</other>
293      </seeother>
294     
295    </helptext>
296  </sect2>
297
298</sect1>
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