source: plugins/base2/net.sf.basedb.normalizers/trunk/META-INF/extensions.xml @ 2176

Last change on this file since 2176 was 2176, checked in by Jari Häkkinen, 9 years ago

Changes from release procedure and other minor things.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 5.8 KB
1<?xml version="1.0" encoding="UTF-8" ?>
3    $Id: extensions.xml 2176 2013-12-12 10:39:47Z jari $
5    Copyright (C) 2011 Nicklas Nordborg
6    Copyright (C) 2013 Jari Häkkinen, Olle Månsson
8    This file is part of the Normalizers plug-in package for BASE
9    (net.sf.based.normalizers). The package is available at
10 BASE main site is
13    This is free software; you can redistribute it and/or modify it
14    under the terms of the GNU General Public License as published by
15    the Free Software Foundation; either version 3 of the License, or
16    (at your option) any later version.
18    The software is distributed in the hope that it will be useful,
19    but WITHOUT ANY WARRANTY; without even the implied warranty of
21    General Public License for more details.
23    You should have received a copy of the GNU General Public License
24    along with this program. If not, see <>.
27<extensions xmlns="">
28  <about>
29    <name>Normalization plug-ins package</name>
30    <description>
31      This package is a compilation of normalisers for expression data.
32      Common to most of the plug-ins is that they work on bioassay sets
33      with either 1-channel or 2-channel data. The algorithms are working
34      on expression values, that is for 2-channel data, ratio ch1/ch2 are
35      used.
36    </description>
37    <version>1.1-beta2</version>
38    <min-base-version>3.2.4</min-base-version>
39    <copyright>BASE development team</copyright>
40    <email></email>
41    <url></url>
42  </about>
44  <plugin-definition id="AverageNormalization">
45    <about>
46      <name>Average normalization</name>
47      <description>
48        This plug-in scales the expression values for an assay with a
49        factor, "S", equal to the ratio of either:
51        i) the geometric mean of the expression values of all spots in the
52        bioassay set divided by the assay average, or
54        ii) a user defined value divided by the assay average.
56        The new expression values will become "S" times the original
57        expression value. Background subtraction and proper filtration
58        have to be done before running this plug-in.
60        This plug-in supports 1-channel and 2-channel data.
61      </description>     
62    </about>   
63    <plugin-class>net.sf.basedb.plugins.AverageNormalization</plugin-class>
64    <settings>
65      <property name="everyone-use">1</property>
66    </settings>
67  </plugin-definition>
69  <plugin-definition id="QuantileNormalization">
70    <about>
71      <name>Quantile normalization</name>
72      <description>
73        In quantile normalization each assay data is sorted in ascending
74        expression value order and added to a matrix as columns. The matrix
75        rows will contain mixed probes (also known as reporters or genes)
76        decided by their rank. For each row in the matrix, the expression
77        values are replaced with the row average value (geometric or
78        arithmetic selectable by user). Finally, each assay is
79        is reordered into its original order to retain a standard
80        expression matrix where each row represents one probe. Assays are
81        not mixed.
83        Background subtraction and proper filtration should be done on the
84        bioassay set before running this plug-in. The bioassay set must not
85        contain any missing values.
87        This plug-in supports 1-channel and 2-channel data.
88      </description>     
89    </about>   
90    <plugin-class>net.sf.basedb.plugins.QuantileNormalization</plugin-class>
91    <settings>
92      <property name="everyone-use">1</property>
93    </settings>
94  </plugin-definition>
96  <plugin-definition id="qQuantileNormalization">
97    <about>
98      <name>qQuantile normalization</name>
99      <description>
100        The qQuantile normalization is inspired by the 'Cubic Spline' normalization
101        in Illumina Beadstudio and the work by Workman et al.,
104        In qQuantile normalization, all assays (including the target) are sorted in
105        increasing intensity. The sorted list of probe intensities are partitioned
106        into q groups, and each of theses q groups are adjusted (normalized) with the
107        corresponding target group. After normalization the intensity distribution of
108        each assay will be approximately the same as the target distribution. q is
109        calculated as q=max(10,min(100,target_size/10)). The program will stop if the
110        number of well defined expression values in the target or any of the assays
111        in the set is smaller than q.
113        The target is defined by selecting a subset of the assays in the bioassay set,
114        and the target expression values are the medians of probe intensities over the
115        bioassay set. Probes with no well defined measurements in the bioassay set are
116        simply ignored in target calculation.
118        Since the normalization calculations are based on geometric means and performed
119        in log space the intensities must be positive and larger than 0. Rather than
120        expecting the user of qQuantile normalization to remove such intensity the
121        underlying algorithm silently ignores zero and negative intensities.
123        Background subtraction and proper filtration should be done on the bioassay set
124        before running this plug-in.
126        Only 1-channel data is supported.
127      </description>     
128    </about>
129    <plugin-class>net.sf.basedb.plugins.qQuantileNormalization</plugin-class>
130    <settings>
131      <property name="deprecated">1</property>
132    </settings>
133  </plugin-definition>
135  <plugin-definition id="RankInvariantNormalization">
136    <about>
137      <name>Rank invariant normalization</name>
138      <description>
139        The development of this plug-in is still in progress.
141        This plug-in currently only supports 1-channel data.
142      </description>     
143    </about>   
144    <plugin-class>net.sf.basedb.plugins.RankInvariantNormalization</plugin-class>
145  </plugin-definition>
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