vsn

Variance stabilization and calibration for microarray data

Bioconductor version: Release (2.7)

The package implements a method for normalising microarray intensities, both between colours within array, and between arrays. The method uses a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references (see vignette). The model incorporates data calibration (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

To install this package, start R and enter:

source("http:///biocLite.R")
biocLite("vsn")    

Documentation

PDF	R Script	Introduction to vsn
PDF	R Script	Likelihood Calculations for vsn
PDF	R Script	Verifying and assessing the performance with simulated data

Reference Manual

Details

biocViews	Microarray, OneChannel, TwoChannel, Preprocessing
Depends	Biobase
Imports	methods, affy, limma, lattice
Suggests	affydata, hgu95av2cdf
System Requirements
License	Artistic-2.0
URL	http://www.r-project.org, http://www.ebi.ac.uk/huber
Depends On Me	LVSmiRNA, affyPara, arrayQualityMetrics, cellHTS2, webbioc
Imports Me	Ringo, imageHTS, tilingArray
Suggests Me	Agi4x44PreProcess, BiocCaseStudies, GlobalAncova, adSplit, beadarray, cellHTS, globaltest, limma, lumi, twilight
Version	3.18.0

Package Downloads

Package Source	vsn_3.18.0.tar.gz
Windows Binary	vsn_3.18.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	vsn_3.18.0.tgz
Package Downloads Report	Download Stats