source: trunk/doc/src/docbook/userdoc/rawbioassays.xml @ 3318

Last change on this file since 3318 was 3318, checked in by Nicklas Nordborg, 14 years ago

Split 'Experiments and analysis' into several files.
Wrote 'Scans and images' section and part of 'Raw bioassays' section.

File size: 10.4 KB
Line 
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_analysis.xml 3308 2007-05-08 12:34:07Z nicklas $
7
8  Copyright (C) Authors contributing to this file.
9
10  This file is part of BASE - BioArray Software Environment.
11  Available at http://base.thep.lu.se/
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13  BASE is free software; you can redistribute it and/or
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27-->
28
29<sect1 id="experiments_analysis.rawbioassay">
30  <title>Raw bioassays</title>
31  <para>
32    A <guilabel>Raw bioassay</guilabel> is the representation
33    of the result of analysing one or more images from a
34    <guilabel>Scan</guilabel>. This typically generates a
35    raw data file with lots of measurements for the spots
36    on the hybridization.
37  </para>
38 
39  <para>
40    Creating a new raw bioassay is a two-step process:
41  </para>
42 
43  <orderedlist>
44    <listitem>
45      <para>
46        Create a new raw bioassay item with the
47        <guilabel>New</guilabel> button in the
48        list view.
49      </para>
50    </listitem>
51    <listitem>
52      <para>
53        Upload the file with the raw data and import it
54        to the raw bioassay. See <xref linkend="import_export_data.import" />.
55      </para>
56    </listitem>
57  </orderedlist>
58 
59  <note>
60    <title>Supported file formats</title>
61    BASE has built-in support for most file formats where the data comes
62    in a tab-separated (or similar) form. Data from one hybridization
63    must be in a single file. Support for other file formats
64    mat be added through plug-ins.
65  </note>
66 
67  <sect2 id="experiments_analysis.rawbioassay.properties">
68    <title>Raw bioassay properties</title>
69   
70    <para>
71      A raw bioassay has the following properties:
72    </para>
73
74    <helptext external_id="rawbioassay.edit" title="Edit raw bioassay">
75   
76    <variablelist>
77      <varlistentry>
78        <term><guilabel>Name</guilabel></term>
79        <listitem>
80          <para>
81            The name of the raw bioassay.
82          </para>
83        </listitem>
84      </varlistentry>
85      <varlistentry>
86        <term><guilabel>Raw data type</guilabel></term>
87        <listitem>
88          <para>
89            The type of raw data. This can't be
90            changed after raw data has been
91            imported. <nohelp>See
92            <xref linkend="experiments_analysis.rawdatatypes" />.</nohelp>
93          </para>
94        </listitem>
95      </varlistentry>
96      <varlistentry>
97        <term><guilabel>Array design</guilabel></term>
98        <listitem>
99          <para>
100            The array design used on the array slide (optional).
101            If an array design is specified
102            the import will verify that the raw data has
103            the same reporter on the same position. This
104            prevents mistakes but also speed up analysis
105            since some optimzations can be used.
106            The array design be changed after raw data has been
107            imported.
108          </para>
109        </listitem>
110      </varlistentry>
111      <varlistentry>
112        <term><guilabel>CEL file</guilabel></term>
113        <listitem>
114          <para>
115            Only used for Affymetrix data.
116            <nohelp>See
117            <xref linkend="experiments_analysis.affymetrix" />
118            </nohelp>
119          </para>
120        </listitem>
121      </varlistentry>
122      <varlistentry>
123        <term><guilabel>Scan</guilabel></term>
124        <listitem>
125          <para>
126            The scan this raw bioassay is related to (optional).
127          </para>
128        </listitem>
129      </varlistentry>
130      <varlistentry>
131        <term><guilabel>Software</guilabel></term>
132        <listitem>
133          <para>
134            The software used to analyse the image or images (optional).
135          </para>
136        </listitem>
137      </varlistentry>
138      <varlistentry>
139        <term><guilabel>Protocol</guilabel></term>
140        <listitem>
141          <para>
142            The protocol used when analysing the image(s) (optional).
143            Software parameters may be registered as part of
144            the protocol.
145          </para>
146        </listitem>
147      </varlistentry>
148      <varlistentry>
149        <term><guilabel>Description</guilabel></term>
150        <listitem>
151          <para>
152            A description of the raw bioassay (optional).
153          </para>
154        </listitem>
155      </varlistentry>
156    </variablelist>
157   
158    <seeother>
159      <other external_id="annotations.edit">Annotations</other>
160      <other external_id="annotations.edit.inerited">Inherit annotations</other>
161    </seeother>
162    </helptext> 
163       
164    <para>
165      A raw bioassay can have annotations. Read more about this in
166      <xref linkend="annotations"/>.
167    </para>
168   
169  </sect2>
170 
171  <sect2 id="experiments_analysis.rawbioassay.rawdata">
172    <title>Import raw data</title>
173    <para>
174      Raw data must be imported after you have created the raw
175      bioassay item. The import is handled by plug-ins. To start
176      the import click on the <guibutton>Import&hellip;</guibutton>
177      button on the single-item view for the raw bioassay.
178      If this button doesn't appear it may be because no file
179      format has been specified for the raw data type used by the
180      raw bioassay or that the logged in user doesn't have permission
181      to use the import plug-in or file format.
182      See <xref linkend="import_export_data.import" /> for more
183      information.
184    </para>
185   
186    <note>
187      <title>Affymetrix data</title>
188      Affymterix data is handled differently and is not
189      imported into the database. See <xref linkend="experiments_analysis.affymetrix" />.
190    </note>
191   
192  </sect2>
193
194  <sect2 id="experiments_analysis.rawdatatypes">
195    <title>Raw data types</title>
196    <para>TODO</para>
197   
198    <sect3 id="experiments_analysis.affymetrix">
199      <title>Affymetrix data</title>
200      <para>TODO</para>
201    </sect3>
202   
203  </sect2>
204
205  <sect2 id="experiments_analysis.spotimages">
206    <title>Spot images</title>
207    <para>
208      If you have uploaded the image or images from the scan
209      you may create spot images. Spot images allows you to
210      view the image of each spot separately in the analysis.
211      For this to work the raw data must contain the X and Y
212      coordinates of each spot.
213    </para>
214   
215    <para>
216      After raw data has been imported into the database
217      you will find that a <guibutton>Create spot images&hellip;</guibutton>
218      button appears in the toolbar on the single-item view
219      for the raw bioassay. Click on this button to open
220      a window that allows you to specify parameters for the
221      spot image extraction.
222    </para>
223   
224    <figure id="experiments_analysis.figures.spotimage">
225      <title>Create spot images</title>
226      <screenshot>
227        <mediaobject>
228          <imageobject><imagedata 
229            fileref="figures/create_spot_images.png" format="PNG"
230            /></imageobject>
231        </mediaobject>
232      </screenshot>
233    </figure>
234   
235    <helptext external_id="rawbioassay.edit.spotimages" 
236      title="Create spot images">
237     
238    <variablelist>
239      <varlistentry>
240        <term><guilabel>X/Y scale and offset</guilabel></term>
241        <listitem>
242          <para>
243            For the spot image creation process to be able
244            to find the spots, the X and Y coordinates from
245            the raw data must be converted into image pixel
246            values. The formula used is:
247            <code>pixelX = (rawX - offsetX) / scaleX</code>
248          </para>
249         
250          <important>
251            It is important that you get these values correct,
252            or the spot image creation process may fail or generate
253            incorrect spot images.
254          </important>
255         
256        </listitem>
257      </varlistentry>
258     
259      <varlistentry>
260        <term><guilabel>Spot size</guilabel></term>
261        <listitem>
262          <para>
263            The spot size is given in pixels and is the width and
264            hight around each spot that is large enough to contain
265            the spot without having too much empty space or
266            neighbouring spots around it.
267          </para>
268     
269        </listitem>
270      </varlistentry>
271     
272      <varlistentry>
273        <term><guilabel>Gamma correction</guilabel></term>
274        <listitem>
275          <para>
276            Gamma correction is needed to make the images
277            look good on computer displays. A value between
278            1.8 and 2.2 is usually best.
279            See <ulink url="http://en.wikipedia.org/wiki/Gamma_correction"
280              >http://en.wikipedia.org/wiki/Gamma_correction</ulink>
281            for more information.
282          </para>
283     
284        </listitem>
285      </varlistentry>
286     
287      <varlistentry>
288        <term><guilabel>Quality</guilabel></term>
289        <listitem>
290          <para>
291            The quality setting to use when saving the generated
292            spot images as JPEG images. A value between 0 = poor
293            and 1 = good can be used.
294          </para>
295        </listitem>
296      </varlistentry>
297     
298      <varlistentry>
299        <term><guilabel>Red, green and blue image files</guilabel></term>
300        <listitem>
301          <para>
302            You must select which scanned image files to use for the
303            red, green and blue component of the generated spot images.
304            Use the <guibutton>Select&hellip;</guibutton> buttons
305            to select existing images or upload new ones.
306            The original image files must be 8- or
307            16-bit grey scale images. Some scanners, for
308            example Genepix, can create TIFF files with more than
309            one image in each file. BASE supports this and uses
310            the images in the order they appear in the TIFF file.
311          </para>
312         
313          <note>
314            Avoid TIFF images which also contains previews
315            of the full image. BASE may use the wrong image
316            with an error as the result. If you have multi-image
317            TIFF files these must only contain the full images.
318          </note>
319         
320        </listitem>
321      </varlistentry>
322      <varlistentry>
323        <term><guilabel>Save as</guilabel></term>
324        <listitem>
325          <para>
326            Specify the path and filename where the generated spot
327            images should be saved. The process will create
328            a single zip file containing all the images.
329          </para>
330        </listitem>
331      </varlistentry>
332     
333      <varlistentry>
334        <term><guilabel>Overwrite existing file</guilabel></term>
335        <listitem>
336          <para>
337            If a file with the same name already exists you
338            must mark this checkbox to overwrite it.
339          </para>
340        </listitem>
341      </varlistentry>
342    </variablelist>
343   
344    <para>
345      Click on the <guibutton>Create</guibutton> button
346      to add the spot image creation job to the job queue,
347      or on <guibutton>Cancel</guibutton> to abort.
348    </para>
349   
350    </helptext>
351  </sect2>
352</sect1>
353   
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