Package: vsn
Version: 3.8.0
Title: Variance stabilization and calibration for microarray data
Author: Wolfgang Huber <huber@ebi.ac.uk>, with contributions from A.
        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 (>= 2.6.0), methods, lattice, Biobase (>= 1.15.33), affy (>=
        1.15.7), limma (>= 2.11.12)
Suggests: affydata, hgu95av2cdf, geneplotter
Description: The package implements a robust variant of the
        maximum-likelihood estimator for the stochastic model of
        microarray data described in the references. The model
        incorporates data calibration (aka 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
        S&uuml;ultmann, 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
        S&uuml;ltmann, 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: Fri Apr 10 13:59:11 2009; biocbuild
Built: R 2.8.1; universal-apple-darwin8.11.1; 2009-04-10 18:44:41; unix
