The package implements a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references. The model incorporates data calibration (aka 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 A. 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://bioconductor.org/biocLite.R")
biocLite("vsn")
Vignettes (Documentation) |
Package Downloads |
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| biocViews | |
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| Depends | R, methods, lattice, Biobase, affy, limma |
| Suggests | affydata, hgu95av2cdf, geneplotter |
| Imports | |
| SystemRequirements | |
| License | Artistic-2.0 |
| URL | http://www.r-project.org, http://www.ebi.ac.uk/huber |
| dependsOnMe | Ringo, arrayQualityMetrics, cellHTS2, tilingArray, webbioc |
| suggestsMe | BiocCaseStudies, GlobalAncova, adSplit, beadarray, cellHTS, ecolitk, globaltest, limma, lumi, twilight |