source: trunk/doc/src/docbook/userdoc/rawbioassays.xml @ 3487

Last change on this file since 3487 was 3487, checked in by Peter Johansson, 15 years ago

added end-of-line style property and replaced don't and similiar with do not and corresponding expression

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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: rawbioassays.xml 3487 2007-06-13 17:56:05Z peter $
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/
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 2
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 this program; if not, write to the Free Software
25  Foundation, Inc., 59 Temple Place - Suite 330,
26  Boston, MA  02111-1307, USA.
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 cannot 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 when assigning
106            positions in bioassay sets.
107            The array design cannot be changed after raw data has been
108            imported.
109          </para>
110        </listitem>
111      </varlistentry>
112      <varlistentry>
113        <term><guilabel>CEL file</guilabel></term>
114        <listitem>
115          <para>
116            Only used for Affymetrix data.
117            <nohelp>See
118            <xref linkend="experiments_analysis.affymetrix" />
119            </nohelp>
120          </para>
121        </listitem>
122      </varlistentry>
123      <varlistentry>
124        <term><guilabel>Scan</guilabel></term>
125        <listitem>
126          <para>
127            The scan this raw bioassay is related to (optional).
128          </para>
129        </listitem>
130      </varlistentry>
131      <varlistentry>
132        <term><guilabel>Software</guilabel></term>
133        <listitem>
134          <para>
135            The software used to analyse the image or images (optional).
136          </para>
137        </listitem>
138      </varlistentry>
139      <varlistentry>
140        <term><guilabel>Protocol</guilabel></term>
141        <listitem>
142          <para>
143            The protocol used when analysing the image(s) (optional).
144            Software parameters may be registered as part of
145            the protocol.
146          </para>
147        </listitem>
148      </varlistentry>
149      <varlistentry>
150        <term><guilabel>Description</guilabel></term>
151        <listitem>
152          <para>
153            A description of the raw bioassay (optional).
154          </para>
155        </listitem>
156      </varlistentry>
157    </variablelist>
158   
159    <seeother>
160      <other external_id="annotations.edit">Annotations</other>
161      <other external_id="annotations.edit.inerited">Inherit annotations</other>
162    </seeother>
163    </helptext> 
164       
165    <para>
166      A raw bioassay can have annotations. Read more about this in
167      <xref linkend="annotations"/>.
168    </para>
169   
170  </sect2>
171 
172  <sect2 id="experiments_analysis.rawbioassay.rawdata">
173    <title>Import raw data</title>
174    <para>
175      Raw data must be imported after you have created the raw
176      bioassay item. The import is handled by plug-ins. To start
177      the import click on the <guibutton>Import&hellip;</guibutton>
178      button on the single-item view for the raw bioassay.
179      If this button does not appear it may be because no file
180      format has been specified for the raw data type used by the
181      raw bioassay or that the logged in user does not have permission
182      to use the import plug-in or file format.
183      See <xref linkend="import_export_data.import" /> for more
184      information.
185    </para>
186   
187    <note>
188      <title>Affymetrix data</title>
189      Affymterix data is handled differently and is not
190      imported into the database. See <xref linkend="experiments_analysis.affymetrix" />.
191    </note>
192   
193  </sect2>
194
195  <sect2 id="experiments_analysis.rawdatatypes">
196    <title>Raw data types</title>
197    <para>TODO</para>
198   
199    <sect3 id="experiments_analysis.affymetrix">
200      <title>Affymetrix data</title>
201      <para>TODO</para>
202    </sect3>
203   
204  </sect2>
205
206  <sect2 id="experiments_analysis.spotimages">
207    <title>Spot images</title>
208    <para>
209      If you have uploaded the image or images from the scan
210      you may create spot images. Spot images allows you to
211      view the image of each spot separately in the analysis.
212      For this to work the raw data must contain the X and Y
213      coordinates of each spot.
214    </para>
215   
216    <para>
217      After raw data has been imported into the database
218      you will find that a <guibutton>Create spot images&hellip;</guibutton>
219      button appears in the toolbar on the single-item view
220      for the raw bioassay. Click on this button to open
221      a window that allows you to specify parameters for the
222      spot image extraction.
223    </para>
224   
225    <figure id="experiments_analysis.figures.spotimage">
226      <title>Create spot images</title>
227      <screenshot>
228        <mediaobject>
229          <imageobject><imagedata 
230            fileref="figures/create_spot_images.png" format="PNG"
231            /></imageobject>
232        </mediaobject>
233      </screenshot>
234    </figure>
235   
236    <helptext external_id="rawbioassay.edit.spotimages" 
237      title="Create spot images">
238     
239    <variablelist>
240      <varlistentry>
241        <term><guilabel>X/Y scale and offset</guilabel></term>
242        <listitem>
243          <para>
244            For the spot image creation process to be able
245            to find the spots, the X and Y coordinates from
246            the raw data must be converted into image pixel
247            values. The formula used is:
248            <code>pixelX = (rawX - offsetX) / scaleX</code>
249          </para>
250         
251          <important>
252            It is important that you get these values correct,
253            or the spot image creation process may fail or generate
254            incorrect spot images.
255          </important>
256         
257        </listitem>
258      </varlistentry>
259     
260      <varlistentry>
261        <term><guilabel>Spot size</guilabel></term>
262        <listitem>
263          <para>
264            The spot size is given in pixels and is the width and
265            hight around each spot that is large enough to contain
266            the spot without having too much empty space or
267            neighbouring spots around it.
268          </para>
269     
270        </listitem>
271      </varlistentry>
272     
273      <varlistentry>
274        <term><guilabel>Gamma correction</guilabel></term>
275        <listitem>
276          <para>
277            Gamma correction is needed to make the images
278            look good on computer displays. A value between
279            1.8 and 2.2 is usually best.
280            See <ulink url="http://en.wikipedia.org/wiki/Gamma_correction"
281              >http://en.wikipedia.org/wiki/Gamma_correction</ulink>
282            for more information.
283          </para>
284     
285        </listitem>
286      </varlistentry>
287     
288      <varlistentry>
289        <term><guilabel>Quality</guilabel></term>
290        <listitem>
291          <para>
292            The quality setting to use when saving the generated
293            spot images as JPEG images. A value between 0 = poor
294            and 1 = good can be used.
295          </para>
296        </listitem>
297      </varlistentry>
298     
299      <varlistentry>
300        <term><guilabel>Red, green and blue image files</guilabel></term>
301        <listitem>
302          <para>
303            You must select which scanned image files to use for the
304            red, green and blue component of the generated spot images.
305            Use the <guibutton>Select&hellip;</guibutton> buttons
306            to select existing images or upload new ones.
307            The original image files must be 8- or
308            16-bit grey scale images. Some scanners, for
309            example Genepix, can create TIFF files with more than
310            one image in each file. BASE supports this and uses
311            the images in the order they appear in the TIFF file.
312          </para>
313         
314          <note>
315            Avoid TIFF images which also contains previews
316            of the full image. BASE may use the wrong image
317            with an error as the result. If you have multi-image
318            TIFF files these must only contain the full images.
319          </note>
320         
321        </listitem>
322      </varlistentry>
323      <varlistentry>
324        <term><guilabel>Save as</guilabel></term>
325        <listitem>
326          <para>
327            Specify the path and filename where the generated spot
328            images should be saved. The process will create
329            a single zip file containing all the images.
330          </para>
331        </listitem>
332      </varlistentry>
333     
334      <varlistentry>
335        <term><guilabel>Overwrite existing file</guilabel></term>
336        <listitem>
337          <para>
338            If a file with the same name already exists you
339            must mark this checkbox to overwrite it.
340          </para>
341        </listitem>
342      </varlistentry>
343    </variablelist>
344   
345    <para>
346      Click on the <guibutton>Create</guibutton> button
347      to add the spot image creation job to the job queue,
348      or on &gbCancel; to abort.
349    </para>
350   
351    </helptext>
352  </sect2>
353</sect1>
354   
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