Package: vsn
Version: 3.58.0
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 <wolfgang.huber@embl.de>
Depends: R (>= 3.4.0), Biobase
Imports: methods, affy, limma, lattice, ggplot2
Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, dplyr, testthat
Description: The package implements a method for normalising microarray intensities, and works
        for single- and multiple-color arrays. It can also be used
	for data from other technologies, as long as they have similar format. The method uses a
	robust variant of the maximum-likelihood estimator for an additive-multiplicative error
	model and affine calibration. The model incorporates data calibration step (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
VignetteBuilder: knitr
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 normalize.AffyBatch.vsn.R sagmbSimulateData.R
        zzz.R
git_url: https://git.bioconductor.org/packages/vsn
git_branch: RELEASE_3_12
git_last_commit: a451e6a
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-27
NeedsCompilation: yes
Packaged: 2020-10-28 04:14:21 UTC; biocbuild
Built: R 4.0.3; x86_64-conda-linux-gnu; 2020-10-30 16:07:44 UTC; unix
