DOI: 10.18129/B9.bioc.vsn  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see vsn.

Variance stabilization and calibration for microarray data

Bioconductor version: 3.16

The package implements a method for normalising microarray intensities from 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.

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 at embl.org>

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HTML R Script Introduction to vsn (HTML version)
PDF R Script Likelihood Calculations for vsn
PDF Verifying and assessing the performance with simulated data
PDF   Reference Manual
Text   NEWS


biocViews Microarray, OneChannel, Preprocessing, Software, TwoChannel
Version 3.66.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 18 years)
License Artistic-2.0
Depends R (>= 4.0.0), methods, Biobase
Imports affy, limma, lattice, ggplot2
Suggests affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr, testthat
URL http://www.r-project.org http://www.ebi.ac.uk/huber
Depends On Me cellHTS2, protGear, rnaseqGene, webbioc
Imports Me arrayQualityMetrics, bnem, coexnet, DEP, Doscheda, ExpressionNormalizationWorkflow, imageHTS, MatrixQCvis, metaseqR2, MSnbase, NormalyzerDE, pvca, Ringo, tilingArray
Suggests Me adSplit, beadarray, DAPAR, DESeq2, estrogen, flowVS, ggbio, GlobalAncova, globaltest, limma, lumi, MsCoreUtils, PAA, QFeatures, qmtools, scp, twilight
Links To Me
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Source Package vsn_3.66.0.tar.gz
Windows Binary vsn_3.66.0.zip (64-bit only)
macOS Binary (x86_64) vsn_3.66.0.tgz
macOS Binary (arm64) vsn_3.66.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/vsn
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/vsn
Bioc Package Browser https://code.bioconductor.org/browse/vsn/
Package Short Url https://bioconductor.org/packages/vsn/
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