Package: vsn
Version: 3.36.0
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 <huber@ebi.ac.uk>
Depends: R (>= 2.10), Biobase (>= 2.5.5)
Imports: methods, affy (>= 1.23.4), limma, lattice
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, http://www.ebi.ac.uk/huber
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: 2015-04-17 01:39:29 UTC; biocbuild
Built: R 3.2.0; x86_64-apple-darwin13.4.0; 2015-04-17 15:35:23 UTC; unix
