To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("vsn")

In most cases, you don't need to download the package archive at all.

vsn

   

This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see vsn.

Variance stabilization and calibration for microarray data

Bioconductor version: 3.3

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 <whuber at embl.de>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("vsn")

Documentation

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

browseVignettes("vsn")

 

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

Details

biocViews Microarray, OneChannel, Preprocessing, Software, TwoChannel
Version 3.40.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 11.5 years)
License Artistic-2.0
Depends R (>= 2.10), Biobase
Imports methods, affy, limma, lattice, ggplot2 (>= 2.0.0), hexbin
LinkingTo
Suggests affydata, hgu95av2cdf
SystemRequirements
Enhances
URL http://www.r-project.org http://www.ebi.ac.uk/huber
Depends On Me affyPara, cellHTS2, MmPalateMiRNA, webbioc
Imports Me arrayQualityMetrics, iCheck, imageHTS, LVSmiRNA, metaseqR, metaX, MSnbase, pvca, Ringo, tilingArray
Suggests Me adSplit, beadarray, BiocCaseStudies, cellHTS, DESeq, DESeq2, estrogen, flowVS, ggbio, GlobalAncova, globaltest, limma, lumi, PAA, twilight
Build Report  

Package Archives

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

Package Source vsn_3.40.0.tar.gz
Windows Binary vsn_3.40.0.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks) vsn_3.40.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/vsn/tree/release-3.3
Package Short Url http://bioconductor.org/packages/vsn/
Package Downloads Report Download Stats

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