source: plugins/base2/net.sf.basedb.normalizers/trunk/README @ 1064

Last change on this file since 1064 was 1064, checked in by Jari Häkkinen, 13 years ago

Addresses #118. Calculate target with median instead of mean.

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[909]1$Id: README 1064 2009-05-14 10:26:03Z jari $
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
[933]8plug-ins in this package. Common to the plug-ins provided with this
[909]9package is that they work on bioassay set with either 1-channel or
[933]102-channel. The algorithms are working on expression values, that is
[925]11for 2-channel data, ratios 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.
45
[909]46Background subtraction and proper filtration have to be done before
[925]47running this plug-in.
[909]48
49
[952]50== qQuantile normalization ==
51
[1064]52qQN geometric mean non-logged values!
53qQN must have positive numbers!
[952]54
[1064]55The assays are normed against a selectable sub-set of the assays
56... If a probe has no well-defined measurement (i.e., no assay in
57the reference has a well defined value for a probe) it is simply
58ignored from the target distribution.
59
60Ja, jag tankte att man far justera q till maximalt antal icke nan ...
61men som sagt an sa lange ar q==100.
62
63Den begränsning som finns nu är att det måste finnas lagom många
64väldefinierade mätvärden per assay (några hundra per assay) annars
65kraschar nog programmet. Jag kommer att lösa detta genom att välja
66antalet bins i distributionsberäkningen som #bins=max(100,N_i/10)
67i=1...#assays och kräva att #bins är minst 10. Kravet är alltså att
68varje assay måste ha minst 100 väldefinierade punkter. Om inte kravet
69är uppfyllt stannar programmet med ett någorlunda trevligt meddelande.
70
71In q-quantile normalization each assay data is sorted in ascending
72expression value order and added to a matrix as columns. The matrix
73rows will contain mixed probes (also known as reporters or genes)
74decided by their rank. For each row in the matrix, the expression
75values are replaced with the row average value. Finally, each assay is
76reordered into its original order to retain a standard expression
77matrix were each row represents one probe. Assays are not mixed.
78
79Background subtraction and proper filtration should be done on the
80bioassay set before running this plug-in. The bioassay set must not
81contain any missing values.
82
[952]83The qQuantile normalization is inspired by the 'Cubic Spline'
84normalization in Illumina Beadstudio and the work by Workman et al.,
85http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12225587
86
87
[926]88== Quantile normalization ==
[909]89
[926]90In quantile normalization each assay data is sorted in ascending
91expression value order and added to a matrix as columns. The matrix
92rows will contain mixed probes (also known as reporters or genes)
93decided by their rank. For each row in the matrix, the expression
94values are replaced with the row average value. Finally, each assay is
95reordered into its original order to retain a standard expression
96matrix were each row represents one probe. Assays are not mixed.
[909]97
[1051]98Background subtraction and proper filtration should be done on the
[909]99bioassay set before running this plug-in. The bioassay set must not
100contain any missing values.
101
[733]102----------------------------------------------------------------------
103{{{
[909]104Copyright (C) 2008 Jari Häkkinen, Martin Svensson
[1051]105Copyright (C) 2009 Jari Häkkinen
[733]106
[909]107This file is part of the Normalizers plug-in package for BASE
108(net.sf.based.normalizers). The package is available at
109http://baseplugins.thep.lu.se/ BASE main site is
110http://base.thep.lu.se/
[733]111
112This is free software; you can redistribute it and/or
113modify it under the terms of the GNU General Public License
[910]114as published by the Free Software Foundation; either version 3
[733]115of the License, or (at your option) any later version.
116
117The software is distributed in the hope that it will be useful,
118but WITHOUT ANY WARRANTY; without even the implied warranty of
119MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
120GNU General Public License for more details.
121
122You should have received a copy of the GNU General Public License
[910]123along with this program. If not, see <http://www.gnu.org/licenses/>.
[733]124}}}
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