vsn: Variance stabilization and calibration for microarray data

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("vsn")
AuthorWolfgang 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
Bioconductor views Microarray OneChannel Preprocessing TwoChannel
Date of publicationNone
MaintainerWolfgang Huber <whuber@embl.de>
LicenseArtistic-2.0
Version3.42.3
http://www.r-project.org
http://www.ebi.ac.uk/huber

View on Bioconductor

Functions

class:vsn Man page
class:vsnInput Man page
coefficients,vsn-method Man page
coef,vsn-method Man page
coerce,RGList,NChannelSet-method Man page
dim,vsnInput-method Man page
dim,vsn-method Man page
exprs,vsn-method Man page
justvsn Man page
kidney Man page
logLik-methods Man page
logLik,vsnInput-method Man page
lymphoma Man page
meanSdPlot Man page
meanSdPlot,ExpressionSet-method Man page
meanSdPlot,MAList-method Man page
meanSdPlot,matrix-method Man page
meanSdPlot-methods Man page
meanSdPlot,vsn-method Man page
ncol,vsnInput-method Man page
ncol,vsn-method Man page
normalize.AffyBatch.vsn Man page
nrow,vsnInput-method Man page
nrow,vsn-method Man page
plotVsnLogLik Man page
predict,vsn-method Man page
sagmbAssess Man page
sagmbSimulateData Man page
scalingFactorTransformation Man page
show,vsnInput-method Man page
show,vsn-method Man page
vsn Man page
vsn2 Man page
vsn2,AffyBatch-method Man page
vsn2,ExpressionSet-method Man page
vsn2,matrix-method Man page
vsn2-methods Man page
vsn2,NChannelSet-method Man page
vsn2,numeric-method Man page
vsn2,RGList-method Man page
vsn-class Man page
vsnh Man page
vsnInput Man page
vsnInput-class Man page
[,vsnInput-method Man page
vsnMatrix Man page
[,vsn-method Man page
vsn-package Man page
vsnPlotPar Man page
vsnrma Man page

Files

.Rinstignore
DESCRIPTION
NAMESPACE
R
R/AllClasses.R R/AllGenerics.R R/RGList_to_NChannelSet.R R/getIntensityMatrix.R R/justvsn.R R/meanSdPlot-methods.R R/methods-predict.R R/methods-vsn.R R/methods-vsn2.R R/methods-vsnInput.R R/normalize.AffyBatch.vsn.R R/plotLikelihood.R R/sagmbSimulateData.R R/vsn.R R/vsn2.R R/vsnLogLik.R R/vsnPlotPar.R R/vsnh.R R/zzz.R
build
build/vignette.rds
data
data/kidney.RData
data/lymphoma.RData
inst
inst/CITATION
inst/doc
inst/doc/A-vsn.R
inst/doc/A-vsn.Rnw
inst/doc/A-vsn.pdf
inst/doc/C-likelihoodcomputations.R
inst/doc/C-likelihoodcomputations.Rnw
inst/doc/C-likelihoodcomputations.pdf
inst/doc/D-convergence.Rnw
inst/doc/D-convergence.pdf
inst/doc/vsn.R
inst/doc/vsn.Rmd
inst/doc/vsn.html
inst/scripts
inst/scripts/README
inst/scripts/convergence.Rnw
inst/scripts/lymphomasamples.txt
inst/scripts/makedata.R inst/scripts/swirl.R inst/scripts/testderiv.R inst/scripts/testmlest.R inst/scripts/testprofiling.R
inst/vignettes
inst/vignettes/4-convergence.Rnw
inst/vignettes/4-convergence.pdf
man
man/class.vsn.Rd man/class.vsnInput.Rd man/justvsn.Rd man/kidney.Rd man/lymphoma.Rd man/meanSdPlot.Rd man/normalize.AffyBatch.vsn.Rd man/sagmbSimulateData.Rd man/scalingFactorTransformation.Rd man/vsn-package.Rd man/vsn.Rd man/vsn2.Rd man/vsn2trsf.Rd man/vsnLikelihood.Rd man/vsnPlotPar.Rd man/vsnh.Rd
src
src/init.c
src/vsn.c
src/vsn.h
src/vsn2.c
vignettes
vignettes/A-vsn.Rnw
vignettes/C-likelihoodcomputations.Rnw
vignettes/D-convergence.Rnw
vignettes/vsn.Rmd
vignettes/vsn.bib

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