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This is the development version of vsn; for the stable release version, see vsn.

Variance stabilization and calibration for microarray data

Bioconductor version: Development (3.20)

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>

Citation (from within R, enter citation("vsn")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews Microarray, OneChannel, Preprocessing, Software, TwoChannel
Version 3.73.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19 years)
License Artistic-2.0
Depends R (>= 4.0.0), methods, Biobase
Imports affy, limma, lattice, ggplot2
System Requirements
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Suggests affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr, testthat
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Depends On Me webbioc, rnaseqGene
Imports Me arrayQualityMetrics, autonomics, bnem, DEP, Doscheda, MatrixQCvis, metaseqR2, MSnbase, NormalyzerDE, pvca, tilingArray, ExpressionNormalizationWorkflow, lfproQC
Suggests Me adSplit, beadarray, DAPAR, DESeq2, ggbio, GlobalAncova, globaltest, limma, lumi, MsCoreUtils, PAA, QFeatures, qmtools, ribosomeProfilingQC, scp, twilight, estrogen, wrMisc
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Source Package vsn_3.73.0.tar.gz
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macOS Binary (x86_64) vsn_3.73.0.tgz
macOS Binary (arm64) vsn_3.73.0.tgz
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