Package: vsn
Version: 2.2.0
Title: Variance stabilization and calibration for microarray data
Author: Wolfgang Huber <huber@ebi.ac.uk>, contributions from A. von
        Heydebreck <heydebre@molgen.mpg.de>, Markus Ruschhaupt
        <m.ruschhaupt@dkfz-heidelberg.de>, D. Kostka
        <dennis.kostka@molgen.mpg.de>
Maintainer: Wolfgang Huber <huber@ebi.ac.uk>
Depends: R (>= 2.5.0), Biobase (>= 1.4.14), methods, affy, limma
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 License 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
        methods-vsnInput.R methods-vsn.R methods-justvsn.R
        meanSdPlot-methods.R plotLikelihood.R vsnPlotPar.R vsn.R vsnh.R
        getIntensityMatrix.R normalize.AffyBatch.vsn.R
        sagmbSimulateData.R zzz.R
Packaged: Wed Apr 25 03:15:55 2007; biocbuild
Built: R 2.5.0; i386-pc-mingw32; 2007-04-25 07:47:31; windows
