source: trunk/doc/historical/test/merge/index.html @ 7982

Last change on this file since 7982 was 7982, checked in by Nicklas Nordborg, 22 months ago

Merge BASE 3.18.2 to the trunk
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1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
2<!--
3  $Id: index.html 7982 2021-06-14 08:01:21Z nicklas $
4
5  Copyright (C) 2006 Nicklas Nordborg
6
7  This file is part of BASE - BioArray Software Environment.
8  Available at http://base.thep.lu.se/
9
10  BASE is free software; you can redistribute it and/or
11  modify it under the terms of the GNU General Public License
12  as published by the Free Software Foundation; either version 3
13  of the License, or (at your option) any later version.
14
15  BASE is distributed in the hope that it will be useful,
16  but WITHOUT ANY WARRANTY; without even the implied warranty of
17  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
18  GNU General Public License for more details.
19
20  You should have received a copy of the GNU General Public License
21  along with BASE. If not, see <http://www.gnu.org/licenses/>.
22-->
23<html>
24  <head>
25    <title>BASE - Test procedures for merged data</title>
26  <link rel=stylesheet type="text/css" href="../../styles.css">
27  </head>
28<body>
29
30<div class="navigation">
31  <a href="../../index.html">BASE</a>
32  <img src="../../next.gif">
33  <a href="../index.html">Test procedures</a>
34  <img src="../../next.gif">
35  Merged data
36</div>
37
38  <h1>Test procedures for merged data</h1>
39
40  <div class="abstract">
41    <p>
42      One of the new features of BASE 2 is that it keeps
43      track of all links back to the raw data for each spot
44      in a bioassayset. In BASE 1 this the link was limited to
45      one raw data for each spot. When doing a merge of spots
46      having, for example, the same reporter it was impossible to
47      keep the link to all raw data that spot was calculated from.
48      You could choose to link to one of the spots or to none at
49      all. With BASE 2 it is possible to keep all the links but
50      it creates some other problems which must be solved:
51    </p>
52   
53    <ul>
54    <li>How to list spot data and raw data at the same time when spot data comes from
55      more than one raw data</li>
56    <li>How to filter spot data on one or more of it's raw data properties</li>
57    <li>How to analyse spot data when raw data is needed for the analysis</li>
58    </ul>
59   
60    <p>
61      It is actually more or less the same problem. How do we select a raw data
62      value when there is many to choose from? Should we always average or do
63      we need other options (max, min, sum, count, etc)?
64    </p>
65   
66    <b>Contents</b><br>
67    <ol>
68    <li><a href="#summary">Summary of the test procedure</a></li>
69    </ol>
70   
71    <b>See also</b><br>
72    <ol>
73    <li><a href="https://base.thep.lu.se/ticket/215">Ticket #215: Incorrect use of
74      DynamicSpotQuery in table view, plot function, filter function, etc.</a>
75    </ol>
76   
77    <p class="authors">
78    <b>Last updated:</b> $Date: 2021-06-14 08:01:21 +0000 (Mon, 14 Jun 2021) $
79    </p>
80  </div>
81
82 
83  <a name="summary"></a>
84  <h2>1. Summary of the test procedure</h2>
85
86  <p>
87    This test procedure sets up an experiment with some merged data. After that
88    it is expected that the web interface is used for trying out various
89    ideas and testing that the desired functionality is working correctly.
90  </p>
91
92  <ol>
93  <li>We recommend starting with a fresh installation, though it is relly neccesary.</li>
94 
95  <li>The test is running as the root user which must have the password "root".</li>
96 
97  <li>10 reporters are created (if they don't exists): MERGE:0, ... MERGE:9</li>
98 
99  <li>An array design is created with 55 features in ten blocks. The first block
100    has one spot of each reporter, the second block reporters 1 to 9, and so on
101    until the last block which only has reporter 9.</li>
102   
103  <li>Two raw bioassays are created and raw data is generated. We only
104    generate data for the mean foreground intensities. The reporter number
105    modulo 3 is used to up- or downregulate each spot. 0, 3, 6, and 9
106    are downregulated, 2, 5, and 8 are upregulated. A random noise term is
107    also added.
108  </li>
109 
110  <li>An experiment is created and a root bioassayset is created from the
111    mean foreground intensities.
112  </li>
113 
114  <li>Two child bioassaysets are created. One which merge the two bioassays
115    together to one bioassay by taking the mean of the spot intensities for
116    each position. The second bioassayset merges reporters for each bioassay.
117  </li>
118  </ol>
119
120  <p>
121    This test doesn't need any data files.
122  </p>
123 
124  <p>
125    To run the test do the following:
126  </p>
127  <ol>
128   
129    <li>Compile the core and the test programs: <code>ant main test</code>.</li>
130
131    <li>Change to the <code>build/test/</code> directory.</li>
132
133    <li>Run test programs: <code>./test.sh merge &lt;cmds&gt;</code> where
134      <code>&lt;cmds&gt;</code> is one or more of the following:
135      <ul>
136      <li><code>all</code>: run all tests</li>
137      <li><code>setup</code>: run the test that creates the data that is needed</li>
138      </ul>
139     
140      More tests may be added in the future.
141    </li>
142   
143  </ol>
144
145
146</body>
147</html>
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