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

<?xml version="1.0" encoding="UTF-8" ?>
<!--
    $Id: extensions.xml 2176 2013-12-12 10:39:47Z jari $

    Copyright (C) 2011 Nicklas Nordborg
    Copyright (C) 2013 Jari Häkkinen, Olle Månsson

    This file is part of the Normalizers plug-in package for BASE
    (net.sf.based.normalizers). The package is available at
    http://baseplugins.thep.lu.se/ BASE main site is
    http://base.thep.lu.se/

    This is free software; you can redistribute it and/or modify it
    under the terms of the GNU General Public License as published by
    the Free Software Foundation; either version 3 of the License, or
    (at your option) any later version.

    The software is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
    General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program. If not, see <http://www.gnu.org/licenses/>.
-->

<extensions xmlns="http://base.thep.lu.se/extensions.xsd">
  <about>
    <name>Normalization plug-ins package</name>
    <description>
      This package is a compilation of normalisers for expression data. 
      Common to most of the plug-ins is that they work on bioassay sets 
      with either 1-channel or 2-channel data. The algorithms are working 
      on expression values, that is for 2-channel data, ratio ch1/ch2 are 
      used.
    </description>
    <version>1.1-beta2</version>
    <min-base-version>3.2.4</min-base-version>
    <copyright>BASE development team</copyright>
    <email>basedb-users@lists.sourceforge.net</email>
    <url>http://baseplugins.thep.lu.se/wiki/net.sf.basedb.normalizers</url>
  </about>

  <plugin-definition id="AverageNormalization">
    <about>
      <name>Average normalization</name>
      <description>
        This plug-in scales the expression values for an assay with a
        factor, "S", equal to the ratio of either:
        
        i) the geometric mean of the expression values of all spots in the 
        bioassay set divided by the assay average, or 
        
        ii) a user defined value divided by the assay average.
        
        The new expression values will become "S" times the original 
        expression value. Background subtraction and proper filtration 
        have to be done before running this plug-in. 
        
        This plug-in supports 1-channel and 2-channel data.
      </description>      
    </about>    
    <plugin-class>net.sf.basedb.plugins.AverageNormalization</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="QuantileNormalization">
    <about>
      <name>Quantile normalization</name>
      <description>
        In quantile normalization each assay data is sorted in ascending 
        expression value order and added to a matrix as columns. The matrix 
        rows will contain mixed probes (also known as reporters or genes) 
        decided by their rank. For each row in the matrix, the expression 
        values are replaced with the row average value (geometric or 
        arithmetic selectable by user). Finally, each assay is 
        is reordered into its original order to retain a standard 
        expression matrix where each row represents one probe. Assays are 
        not mixed.
        
        Background subtraction and proper filtration should be done on the 
        bioassay set before running this plug-in. The bioassay set must not 
        contain any missing values.
        
        This plug-in supports 1-channel and 2-channel data.
      </description>      
    </about>    
    <plugin-class>net.sf.basedb.plugins.QuantileNormalization</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="qQuantileNormalization">
    <about>
      <name>qQuantile normalization</name>
      <description>
        The qQuantile normalization is inspired by the 'Cubic Spline' normalization 
        in Illumina Beadstudio and the work by Workman et al., 
        http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&amp;pubmedid=12225587

        In qQuantile normalization, all assays (including the target) are sorted in 
        increasing intensity. The sorted list of probe intensities are partitioned 
        into q groups, and each of theses q groups are adjusted (normalized) with the 
        corresponding target group. After normalization the intensity distribution of 
        each assay will be approximately the same as the target distribution. q is 
        calculated as q=max(10,min(100,target_size/10)). The program will stop if the 
        number of well defined expression values in the target or any of the assays 
        in the set is smaller than q.

        The target is defined by selecting a subset of the assays in the bioassay set, 
        and the target expression values are the medians of probe intensities over the 
        bioassay set. Probes with no well defined measurements in the bioassay set are 
        simply ignored in target calculation.

        Since the normalization calculations are based on geometric means and performed 
        in log space the intensities must be positive and larger than 0. Rather than 
        expecting the user of qQuantile normalization to remove such intensity the 
        underlying algorithm silently ignores zero and negative intensities.

        Background subtraction and proper filtration should be done on the bioassay set 
        before running this plug-in.

        Only 1-channel data is supported.
      </description>      
    </about>
    <plugin-class>net.sf.basedb.plugins.qQuantileNormalization</plugin-class>
    <settings>
      <property name="deprecated">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="RankInvariantNormalization">
    <about>
      <name>Rank invariant normalization</name>
      <description>
        The development of this plug-in is still in progress.
        
        This plug-in currently only supports 1-channel data.
      </description>      
    </about>    
    <plugin-class>net.sf.basedb.plugins.RankInvariantNormalization</plugin-class>
  </plugin-definition>

</extensions>