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Package: vsn
Version: 3.40.0
Title: Variance stabilization and calibration for microarray data
Author: Wolfgang Huber, with contributions from Anja von
Heydebreck. Many comments and suggestions by users are
acknowledged, among them Dennis Kostka, David Kreil, Hans-Ulrich
Klein, Robert Gentleman, Deepayan Sarkar and Gordon Smyth
Maintainer: Wolfgang Huber <whuber@embl.de>
Depends: R (>= 2.10), Biobase
Imports: methods, affy, limma, lattice, ggplot2 (>= 2.0.0), hexbin
Suggests: affydata, hgu95av2cdf
Description: The package implements a method for normalising microarray intensities,
both between colours within array, and between arrays. The method uses a
robust variant of the maximum-likelihood estimator for the stochastic model of
microarray data described in the references (see vignette).
The model incorporates data calibration (a.k.a. normalization), a model for
the dependence of the variance on the mean intensity, and a
variance stabilizing data transformation. Differences between
transformed intensities are analogous to "normalized
log-ratios". However, in contrast to the latter, their
variance is independent of the mean, and they are usually more
sensitive and specific in detecting differential
transcription.
Reference: [1] Variance stabilization applied to microarray data
calibration and to the quantification of differential
expression, Wolfgang Huber, Anja von Heydebreck, Holger
Sueltmann, Annemarie Poustka, Martin Vingron; Bioinformatics
(2002) 18 Suppl1 S96-S104. [2] Parameter estimation for the
calibration and variance stabilization of microarray data,
Wolfgang Huber, Anja von Heydebreck, Holger Sueltmann,
Annemarie Poustka, and Martin Vingron; Statistical Applications
in Genetics and Molecular Biology (2003) Vol. 2 No. 1, Article
3; http://www.bepress.com/sagmb/vol2/iss1/art3.
License: Artistic-2.0
URL: http://www.r-project.org
biocViews: Microarray, OneChannel, TwoChannel, Preprocessing
Collate: AllClasses.R AllGenerics.R vsn2.R vsnLogLik.R justvsn.R
methods-vsnInput.R methods-vsn.R methods-vsn2.R
methods-predict.R RGList_to_NChannelSet.R meanSdPlot-methods.R
plotLikelihood.R vsnPlotPar.R vsn.R vsnh.R getIntensityMatrix.R
normalize.AffyBatch.vsn.R sagmbSimulateData.R zzz.R
NeedsCompilation: yes
Packaged: 2016-05-04 02:38:02 UTC; biocbuild
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providing 
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