$Id: README 933 2008-12-18 11:41:56Z jari $
= About `Normalization package for BASE` =
The `Normalization package for BASE (net.sf.basedb.normalization)`
plug-in set is a compilation of normalisers for expression data. See
``Documentation`` below for further information about the different
plug-ins in this package. Common to the plug-ins provided with this
package is that they work on bioassay set with either 1-channel or
2-channel. The algorithms are working on expression values, that is
for 2-channel data, ratios ch1/ch2 are used.
`Normalization package for BASE` is free software. See the file
license.txt for copying conditions.
The package was created by Martin Svensson and Jari Hakkinen.
== Downloading ==
`Normalization package for BASE` can be obtained from
http://baseplugins.thep.lu.se/wiki/PluginDownload
= Installation =
Installation instructions can be found in the 'INSTALL' file.
= Documentation =
== Average normalization ==
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.
== Quantile normalization ==
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. Finally, each assay is
reordered into its original order to retain a standard expression
matrix were each row represents one probe. Assays are not mixed.
Background subtraction and proper filtration have to be done on the
bioassay set before running this plug-in. The bioassay set must not
contain any missing values.
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{{{
Copyright (C) 2008 Jari Häkkinen, Martin Svensson
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 .
}}}