vsn

DOI: 10.18129/B9.bioc.vsn    

Variance stabilization and calibration for microarray data

Bioconductor version: Release (3.13)

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.

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.de>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("vsn")

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

Documentation

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

browseVignettes("vsn")

 

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

Details

biocViews	Microarray, OneChannel, Preprocessing, Software, TwoChannel
Version	3.60.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 16.5 years)
License	Artistic-2.0
Depends	R (>= 3.4.0), Biobase
Imports	methods, affy, limma, lattice, ggplot2
LinkingTo
Suggests	affydata, hgu95av2cdf, BiocStyle, knitr, dplyr, testthat
SystemRequirements
Enhances
URL	http://www.r-project.org http://www.ebi.ac.uk/huber
Depends On Me	affyPara, cellHTS2, rnaseqGene, webbioc
Imports Me	arrayQualityMetrics, bnem, coexnet, DAPAR, DEP, Doscheda, ExpressionNormalizationWorkflow, imageHTS, MatrixQCvis, metaseqR2, MSnbase, NormalyzerDE, pvca, Ringo, tilingArray
Suggests Me	adSplit, beadarray, BiocCaseStudies, DESeq2, estrogen, flowVS, ggbio, GlobalAncova, globaltest, limma, lumi, MsCoreUtils, PAA, QFeatures, scp, twilight
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	vsn_3.60.0.tar.gz
Windows Binary	vsn_3.60.0.zip
macOS 10.13 (High Sierra)	vsn_3.60.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/vsn
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/vsn
Package Short Url	https://bioconductor.org/packages/vsn/
Package Downloads Report	Download Stats