Package: vsn
Version: 3.12.0
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: Biobase (>= 2.3.1)
Imports: methods, affy, 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, see
        http://www.opensource.org/licenses/artistic-license-2.0.php
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
Packaged: 2009-04-21 10:32:05 UTC; biocbuild
Built: R 2.9.0; universal-apple-darwin9.6.0; 2009-04-21 14:58:41 UTC; unix
