vsn: Variance stabilization and calibration for microarray data
Version 3.44.0

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.

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 <wolfgang.huber@embl.de>
LicenseArtistic-2.0
Version3.44.0
URL http://www.r-project.org http://www.ebi.ac.uk/huber
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("vsn")

Getting started

Package overview
Introduction to vsn (HTML version)

Popular man pages

justvsn: Wrapper functions for vsn
kidney: Intensity data for 1 cDNA slide with two adjacent tissue...
lymphoma: Intensity data for 8 cDNA slides with CLL and DLBL samples...
meanSdPlot: Plot row standard deviations versus row means
sagmbSimulateData: Simulate data and assess vsn's parameter estimation
scalingFactorTransformation: The transformation that is applied to the scaling parameter...
vsn: Variance stabilization and calibration for microarray data.
See all...

All man pages Function index File listing

Man pages

class.vsn: Class to contain result of a vsn fit
class.vsnInput: Class to contain input data and parameters for vsn functions
justvsn: Wrapper functions for vsn
kidney: Intensity data for 1 cDNA slide with two adjacent tissue...
lymphoma: Intensity data for 8 cDNA slides with CLL and DLBL samples...
meanSdPlot: Plot row standard deviations versus row means
normalize.AffyBatch.vsn: Wrapper for vsn to be used as a normalization method with...
sagmbSimulateData: Simulate data and assess vsn's parameter estimation
scalingFactorTransformation: The transformation that is applied to the scaling parameter...
vsn: Variance stabilization and calibration for microarray data.
vsn2: Fit the vsn model
vsn2trsf: Apply the vsn transformation to data
vsnh: A function that transforms a matrix of microarray...
vsnLikelihood: Calculate the log likelihood and its gradient for the vsn...
vsn-package: vsn
vsnPlotPar: Plot trajectories of calibration and transformation...

Functions

MatrixFromNChannelSet Source code
[,vsn-method Man page
[,vsnInput-method Man page
calc.istrat Source code
calcistrat Source code
calibCharToInt Source code
checkArgs Source code
class:vsn Man page
class:vsnInput Man page
coef,vsn-method Man page
coefficients,vsn-method Man page
coerce,RGList,NChannelSet-method Man page
dim,vsn-method Man page
dim,vsnInput-method Man page
dovsn Source code
equalOrZero Source code
exprs,vsn-method Man page
getIntensityMatrix Source code
int2factor Source code
isSmall Source code
justvsn Man page Source code
kidney Man page
logLik,vsnInput-method Man page
logLik-methods Man page
lymphoma Man page
meanSdPlot Man page
meanSdPlot,ExpressionSet-method Man page
meanSdPlot,MAList-method Man page
meanSdPlot,matrix-method Man page
meanSdPlot,vsn-method Man page
meanSdPlot-methods Man page
ncol,vsn-method Man page
ncol,vsnInput-method Man page
normalize.AffyBatch.vsn Man page Source code
nrow,vsn-method Man page
nrow,vsnInput-method Man page
onAttach Source code
onLoad Source code
plotVsnLogLik Man page Source code
predict,vsn-method Man page
predict_vsn_NChannelSet Source code
predict_vsn_RGList Source code
predict_vsn_matrix Source code
predict_vsn_numeric Source code
pstartHeuristic Source code
rowV Source code
sagmbAssess Man page Source code
sagmbSimulateData Man page Source code
scalingFactorTransformation Man page Source code
show,vsn-method Man page
show,vsnInput-method Man page
validLogical Source code
validScalarDoubleListElt Source code
validScalarIntListElt Source code
validScalarNumericSlot Source code
validityVsn Source code
validityVsnInput Source code
vsn Man page Man page Source code
vsn-class Man page
vsn-package Man page
vsn2 Man page
vsn2,AffyBatch-method Man page
vsn2,ExpressionSet-method Man page
vsn2,NChannelSet-method Man page
vsn2,RGList-method Man page
vsn2,matrix-method Man page
vsn2,numeric-method Man page
vsn2-methods Man page
vsn2trsf Source code
vsnColumnByColumn Source code
vsnHessian Source code
vsnInput Man page
vsnInput-class Man page
vsnLTS Source code
vsnLogLik Source code
vsnML Source code
vsnMatrix Man page Source code
vsnPlotPar Man page Source code
vsnSample Source code
vsnStrata Source code
vsnh Man page Source code
vsnrma Man page Source code

Files

.Rinstignore
DESCRIPTION
NAMESPACE
NEWS
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
tests
tests/testthat
tests/testthat.R
tests/testthat/test_calib.R
vignettes
vignettes/A-vsn.Rnw
vignettes/C-likelihoodcomputations.Rnw
vignettes/D-convergence.Rnw
vignettes/vsn.Rmd
vignettes/vsn.bib
vsn documentation built on May 20, 2017, 9:23 p.m.

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