source: plugins/base2/net.sf.basedb.normalizers/trunk/README @ 1087

Last change on this file since 1087 was 1087, checked in by Martin Svensson, 12 years ago

Fixes #195 net.sf.basedb.normalizers: Normalizers should ask user for how to calculate averages

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[909]1$Id: README 1087 2009-05-19 12:30:34Z martin $
2
3= About `Normalization package for BASE` =
4
5The `Normalization package for BASE (net.sf.basedb.normalization)`
6plug-in set is a compilation of normalisers for expression data. See
7``Documentation`` below for further information about the different
[1074]8plug-ins in this package. Common to most of the plug-ins provided with
9this package is that they work on bioassay sets with either 1-channel
10and 2-channel data. The algorithms are working on expression values,
11that is for 2-channel data, ratio ch1/ch2 are used.
[909]12
13`Normalization package for BASE` is free software. See the file
14license.txt for copying conditions.
15
[952]16The package was created, and is maintained, by Martin Svensson and
17Jari Hakkinen.
[909]18
19
20== Downloading ==
21
22`Normalization package for BASE` can be obtained from
23
24  http://baseplugins.thep.lu.se/wiki/PluginDownload
25
26
27= Installation =
28
29Installation instructions can be found in the 'INSTALL' file.
30
31
32= Documentation =
33
34
35== Average normalization ==
36
[925]37This plug-in scales the expression values for an assay with a factor,
[928]38''S'', equal to the ratio of either i) the geometric mean of the
39expression values of all spots in the bioassay set divided by the
40assay average, or ii) a user defined value divided by the assay
41average.
[909]42
[925]43The new expression values will become ''S'' times the original
44expression value.
[1087]45The user can choose between using geometric or arithmetic mean when
46calculating the averages.
[925]47
[909]48Background subtraction and proper filtration have to be done before
[925]49running this plug-in.
[909]50
51
[952]52== qQuantile normalization ==
53
[1074]54The current implementation of qQuantile normalization supports only
551-channel arrays.
[952]56
57The qQuantile normalization is inspired by the 'Cubic Spline'
58normalization in Illumina Beadstudio and the work by Workman et al.,
59http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12225587
60
[1074]61In qQuantile normalization, all assays (including the target) are
62sorted in increasing intensity. The sorted list of probe intensities
63are partitioned into q groups, and each of theses q groups are
64adjusted (normalized) with the corresponding target group. After
65normalization the intensity distribution of each assay will be
66approximately the same as the target distribution. q is calculated as
67q=max(10,min(100,target_size/10)). The program will stop if the number
68of well defined expression values in the target or any of the assays
69in the set is smaller than q.
[952]70
[1074]71The target is defined by selecting a subset of the assays in the
72bioassay set, and the target expression values are the medians of
73probe intensities over the bioassay set. Probes with no well defined
74measurements in the bioassay set are simply ignored in target
75calculation.
76
77Since the normalization calculations are based on geometric means and
78performed in log space the intensities must be positive and larger
79than 0. Rather than expecting the user of qQuantile normalization to
80remove such intensity the underlying algorithm silently ignores zero
81and negative intensities.
82
83Background subtraction and proper filtration should be done on the
84bioassay set before running this plug-in.
85
86
[926]87== Quantile normalization ==
[909]88
[926]89In quantile normalization each assay data is sorted in ascending
90expression value order and added to a matrix as columns. The matrix
91rows will contain mixed probes (also known as reporters or genes)
92decided by their rank. For each row in the matrix, the expression
93values are replaced with the row average value. Finally, each assay is
94reordered into its original order to retain a standard expression
95matrix were each row represents one probe. Assays are not mixed.
[909]96
[1051]97Background subtraction and proper filtration should be done on the
[909]98bioassay set before running this plug-in. The bioassay set must not
99contain any missing values.
100
[733]101----------------------------------------------------------------------
102{{{
[909]103Copyright (C) 2008 Jari Häkkinen, Martin Svensson
[1051]104Copyright (C) 2009 Jari Häkkinen
[733]105
[909]106This file is part of the Normalizers plug-in package for BASE
107(net.sf.based.normalizers). The package is available at
108http://baseplugins.thep.lu.se/ BASE main site is
109http://base.thep.lu.se/
[733]110
111This is free software; you can redistribute it and/or
112modify it under the terms of the GNU General Public License
[910]113as published by the Free Software Foundation; either version 3
[733]114of the License, or (at your option) any later version.
115
116The software is distributed in the hope that it will be useful,
117but WITHOUT ANY WARRANTY; without even the implied warranty of
118MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
119GNU General Public License for more details.
120
121You should have received a copy of the GNU General Public License
[910]122along with this program. If not, see <http://www.gnu.org/licenses/>.
[733]123}}}
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