source: trunk/doc/src/docbook/user/rawbioassays.xml @ 7640

Last change on this file since 7640 was 7640, checked in by Nicklas Nordborg, 3 years ago

References #2136: Remove support for spot images

Updated documentation.

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1<?xml version="1.0" encoding="UTF-8"?>
3    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
6  $Id: rawbioassays.xml 7640 2019-03-11 13:13:29Z nicklas $
8  Copyright (C) 2007 Peter Johansson, Nicklas Nordborg, Martin Svensson
10  This file is part of BASE - BioArray Software Environment.
11  Available at
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.
18  BASE is distributed in the hope that it will be useful,
19  but WITHOUT ANY WARRANTY; without even the implied warranty of
21  GNU General Public License for more details.
23  You should have received a copy of the GNU General Public License
24  along with BASE. If not, see <>.
27<sect1 id="experiments_analysis.rawbioassay">
28  <?dbhtml filename="rawbioassays.html" ?>
29  <title>Raw bioassays</title>
30  <para>
31    A <guilabel>Raw bioassay</guilabel> is the representation
32    of the result of analyzing data from the physical bioassay
33    down to the point where we have a file or a set of files
34    containing measurements per feature (eg. spot, gene, etc.)
35    for a single sample or extract. Further analysis is usually
36    needed before we can say something about individual features
37    or samples and how they relate to each other. This
38    kind of analisys is done in <guilabel>Experiments</guilabel>.
39    See <xref linkend="experiments_analysis.experiments" />.
40  </para>
42  <para>
43    The term <guilabel>Raw bioassay</guilabel> is bit misleading since the
44    real "raw data" is actually the images from a microarray scan or the
45    output from a sequencer. For historical reasons we have chosen to keep
46    the term raw bioassay since this represents the first possibility for
47    a transition between file-base data and database-stored data. Typically,
48    all pre-rawbioassay analysis is done outside of BASE, and although
49    we now have the possibility to track this in detail, it will
50    probably remain so for some time in the future. See
51    <xref linkend="experiments_analysis.derivedbioassays" />.
53  </para>
55  <sect2 id="experiments_analysis.rawbioassay.create">
56    <title>Create raw bioassays</title>
57    <para>
58      Creating a new raw bioassay is a two- or three-step process:
59    </para>
61    <orderedlist>
62      <listitem>
63        <para>
64          Create a new raw bioassay item with the &gbNew; button in the raw bioassays list view.
65          It is also possible to create raw bioassays from the derived bioassays
66          list- and single view- page.
67        </para>
68      </listitem>
69      <listitem>
70        <para>
71        Upload the file(s) with the raw data and attach them to the
72        raw bioassay.
73        </para>
74      </listitem>
75      <listitem>
76        <para>
77          The used platform may require that data is imported to the database.
78          See <xref linkend="import_data" />. If the platform is a
79          file-only platform, this step can be skipped.
80        </para>
81      </listitem>
82    </orderedlist>
84    <note>
85      <title>Supported file formats</title>
86      BASE has built-in support for most file formats where the data comes
87      in a tab-separated (or similar) form. Data for one raw bioassay
88      must be in a single file. Support for other file formats
89      may be added through plug-ins.
90    </note>
91  </sect2>
93  <sect2 id="">
94    <title>Raw bioassay properties</title>
96    <figure
97      id="experiments_analysis.figures.rawbioassay.edit">
98      <title>Raw bioassay properties</title>
99      <screenshot>
100        <mediaobject>
101          <imageobject>
102            <imagedata
103              fileref="figures/rawbioassay_edit.png" format="PNG" />
104          </imageobject>
105        </mediaobject>
106      </screenshot>
107    </figure> 
109    <helptext external_id="rawbioassay.edit" title="Edit raw bioassay">
111    <variablelist>
112      <varlistentry>
113        <term><guilabel>Name</guilabel></term>
114        <listitem>
115          <para>
116            The name of the raw bioassay.
117          </para>
118        </listitem>
119      </varlistentry>
120      <varlistentry>
121        <term>
122          <guilabel>Platform</guilabel>
123        </term>
124        <listitem>
125          <para>
126            Select the platform / variant used for the
127            raw bioassay. The selected options affects which
128            files that can be selected on the <guilabel>Data files</guilabel>
129            tab. If the platform supports importing data to the database
130            you must also select a <guilabel>Raw data type</guilabel>.
131          </para>
132        </listitem>
133      </varlistentry>
134      <varlistentry>
135        <term><guilabel>Raw data type</guilabel></term>
136        <listitem>
137          <para>
138            The type of raw data. This option is disabled for file-only
139            platforms and for platforms that are locked to a specific
140            raw data type. This cannot be changed after raw data has been
141            imported. <nohelp>See
142            <xref linkend="experiments_analysis.rawdatatypes" />.</nohelp>
143          </para>
144        </listitem>
145      </varlistentry>
146      <varlistentry>
147        <term><guilabel>Parent bioassay</guilabel></term>
148        <listitem>
149          <para>
150            The derived bioassay that is the parent of this
151            raw bioassay.
152          </para>
153        </listitem>
154      </varlistentry>
155      <varlistentry>
156        <term><guilabel>Parent extract</guilabel></term>
157        <listitem>
158          <para>
159            The extract which this raw bioassay has measured. This is normally selected
160            among the extracts that are linked with the physical bioassay that this
161            raw bioassay is coming from. Selecting the correct extract is important if the
162            physical bioassay contains more than one extract, since otherwise it may affect
163            how annotations are inherited and used in downstream analysis.
164          </para>
165        </listitem>
166      </varlistentry>
167      <varlistentry>
168        <term><guilabel>Array design</guilabel></term>
169        <listitem>
170          <para>
171            The array design used on the array slide (optional).
172            If an array design is specified
173            the import will verify that the raw data has
174            the same reporter on the same position. This
175            prevents mistakes but also speed up analysis
176            since some optimizations can be used when assigning
177            positions in bioassay sets.
178            The array design can be changed after raw data has been
179            imported, but this triggers a new validation. If the raw data
180            is stored in the database, the features on the new array design must
181            match the the raw data. The verification can use three different methods:
182          </para>
184          <itemizedlist>
185          <listitem>
186            <para>
187            Coordinates: Verify block, meta-grid, row and column coordinates.
188            </para>
189          </listitem>
190          <listitem>
191            <para>Position: Verify the position number.</para>
192          </listitem>
193          <listitem>
194            <para>
195            Feature ID: Verify the feature ID. This option can only be used
196            if the raw bioassay is currently connected to an array design that
197            has feature ID values already.
198            </para>
199          </listitem>
200          </itemizedlist>
201          <para>
202            In all three cases it is also verified that the reporter of the raw
203            data matches the reporter of the features.
204          </para>
206          <para>
207            For Affymetrix data, the
208            CEL file is validated against the CDF file of the new array design.
209            If the validation fails, the array design is not changed.
210          </para>
211        </listitem>
212      </varlistentry>
213      <varlistentry>
214        <term><guilabel>Software</guilabel></term>
215        <listitem>
216          <para>
217            The software used to generate the raw data (optional).
218          </para>
219        </listitem>
220      </varlistentry>
221      <varlistentry>
222        <term><guilabel>Protocol</guilabel></term>
223        <listitem>
224          <para>
225            The protocol used when generating the raw data (optional).
226            Software parameters may be registered as part of
227            the protocol.
228          </para>
229        </listitem>
230      </varlistentry>
231      <varlistentry>
232        <term><guilabel>Description</guilabel></term>
233        <listitem>
234          <para>
235            A description of the raw bioassay (optional).
236          </para>
237        </listitem>
238      </varlistentry>
239    </variablelist>
241    <seeother>
242      <other external_id="datafiles.edit">Data files</other>
243      <other external_id="annotations.edit">Annotations</other>
244      <other external_id="annotations.edit.inerited">Inherit annotations</other>
245    </seeother>
246    </helptext> 
249    <para>
250      The <guilabel>Data files</guilabel> tab allows BASE users to select
251      files that contains data for the raw bioassay.
252      Read more about this in <xref linkend="platforms.selectfiles" />.
253    </para>
255    <para>
256      The <guilabel>Annotations</guilabel> tab allows BASE users to use
257      annotation types to refine bioassay description. More about annotating items
258      can be read in <xref linkend="annotations.annotating" />
259    </para>
261    <para>
262      This <guilabel>Inherited annotations</guilabel> tab contains a list of those annotations
263      that are inherited from the bioassay's parents. Information about working with inherited
264      annotations can be found in <xref linkend="annotations.inheriting" />.
265    </para>
267  </sect2>
269  <sect2 id="experiments_analysis.rawbioassay.rawdata">
270    <title>Import raw data</title>
271    <para>
272      Depending on the platform, raw data may have to be imported after
273      you have created the raw bioassay item. This section doesn't apply
274      to file-only platforms. The import is handled by plug-ins. To start
275      the import click on the <guibutton>Import&hellip;</guibutton>
276      button on the single-item view for the raw bioassay.
277      If this button does not appear it may be because no file
278      format has been specified for the raw data type used by the
279      raw bioassay or that the logged in user does not have permission
280      to use the import plug-in or file format.
281      See <xref linkend="import_data" /> for more
282      information.
283    </para>
285    <note>
286      <title>File-only platforms</title>
287      File-only platforms, such as Affymetrix, is handled differently and data is not
288      imported into the database.
289    </note>
291  </sect2>
293  <sect2 id="experiments_analysis.rawdatatypes">
294    <title>Raw data types</title>
296    <para>
297      A raw data type defines the types of measured values that can be stored
298      for individual features in the database. Usually this includes some
299      kind of foreground and background intensity values. The number and meaning
300      of the values usually depends on the hardware and software used to analyze
301      the data from the experiment. Many tools provide mean and median values,
302      standard deviations, quality control information, etc. Since there are so
303      many existing tools with many different data file formats BASE uses a
304      separate database table for each raw data type to store data. The raw data
305      tables have been optimized for the type of raw data they can hold and only
306      has the columns that are needed to store the data. BASE ships with a large
307      number of pre-defined raw data types. An administrator may also define
308      additional raw data type. See <xref linkend="appendix.rawdatatypes" /> 
309      for more information.
310    </para>
312    <sect3 id="experiments_analysis.fileonly">
313      <title>File-only platforms</title>
314      <para>
315        In some cases it doesn't make sense to import any data into the
316        database. The main reason is that performance will suffer as the
317        number of entries in the database gets higher. A typical Genepix file
318        contains ~55K spots while an Affymetrix file may have millions.
319      </para>
320      <para>
321        The drawback of keeping the data in files is that none of the generic
322        tools in BASE can read it. Special plug-ins must be developed for each
323        type of data file that can be used to analyze and visualize the data.
324        For the Affymetrix platform there are implementations of the RMAExpress
325        and Plier normalizations available on the BASE plug-ins web site.
326        BASE also ships with built-in plug-ins for extracting metadata from
327        Affymetrix CEL and CDF files (ie. headers, number of spots, etc).
328      </para>
329      <para>
330        Users of other file-only platforms should check the BASE plug-ins
331        website for plug-ins related to their platform. If they can't
332        find any we recommend that they try to find other users of the same
333        platform and try to cooperate in developing the required tools and
334        plug-ins.
335      </para>
336    </sect3>
338  </sect2>
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