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
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Variance stabilization and calibration for microarray data
Bioconductor version: Release (3.4)
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 <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")
| R Script | Introduction to vsn (Sweave version) | |
| R Script | Likelihood Calculations for vsn | |
| Verifying and assessing the performance with simulated data | ||
| HTML | R Script | Introduction to vsn (HTML version) |
| Reference Manual |
Details
| biocViews | Microarray, OneChannel, Preprocessing, Software, TwoChannel |
| Version | 3.42.3 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 12 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.0.0), Biobase |
| Imports | methods, affy, limma, lattice, ggplot2 |
| LinkingTo | |
| Suggests | affydata, hgu95av2cdf, BiocStyle, knitr |
| SystemRequirements | |
| Enhances | |
| URL | http://www.r-project.org http://www.ebi.ac.uk/huber |
| Depends On Me | affyPara, cellHTS2, MmPalateMiRNA, webbioc |
| Imports Me | arrayQualityMetrics, imageHTS, LVSmiRNA, metaseqR, MSnbase, pvca, Ringo, tilingArray |
| Suggests Me | adSplit, beadarray, BiocCaseStudies, 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_3.42.3.tar.gz |
| Windows Binary | vsn_3.42.3.zip (32- & 64-bit) |
| Mac OS X 10.9 (Mavericks) | vsn_3.42.3.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/vsn/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/vsn/ |
| Package Downloads Report | Download Stats |
Documentation »
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