To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("sva")

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

sva

Surrogate Variable Analysis

Bioconductor version: Release (2.14)

The sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. Specifically, the sva package contains functions for the identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are covariates constructed directly from high-dimensional data (like gene expression/RNA sequencing/methylation/brain imaging data) that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise. The sva package can be used to remove artifacts in two ways: (1) identifying and estimating surrogate variables for unknown sources of variation in high-throughput experiments (Leek and Storey 2007 PLoS Genetics,2008 PNAS) and (2) directly removing known batch effects using ComBat (Johnson et al. 2007 Biostatistics). Removing batch effects and using surrogate variables in differential expression analysis have been shown to reduce dependence, stabilize error rate estimates, and improve reproducibility, see (Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat. Reviews Genetics). Surrogate variable analysis and ComBat were developed in the context of microarray experiments, but may be used as a general tool for high throughput data sets where dependence may be involved.

Author: Jeffrey T. Leek <jleek at jhsph.edu>, W. Evan Johnson <wej at bu.edu>, Hilary S. Parker <hiparker at jhsph.edu>, Andrew E. Jaffe <ajaffe at jhsph.edu>, John D. Storey <jstorey at princeton.edu>,

Maintainer: Jeffrey T. Leek <jleek at jhsph.edu>

To install this package, start R and enter:

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

Installation

source("http://bioconductor.org/biocLite.R")
biocLite("sva")

Documentation

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

browseVignettes("sva")

 

PDF R Script bladderbatchTutorial
PDF   Reference Manual

Details

biocViews Microarray, MultipleComparison, Preprocessing, Software, StatisticalMethod
Version 3.10.0
In Bioconductor since BioC 2.9 (R-2.14)
License Artistic-2.0
Depends R (>= 2.8), corpcor, mgcv
Imports graphics, stats
Suggests limma, pamr, bladderbatch
System Requirements
URL
Depends On Me SCAN.UPC
Imports Me ChAMP, charm, DeSousa2013, trigger
Suggests Me curatedBladderData, curatedCRCData, curatedOvarianData

Package Archives

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

Package Source sva_3.10.0.tar.gz
Windows Binary sva_3.10.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) sva_3.10.0.tgz
Mac OS X 10.9 (Mavericks) sva_3.10.0.tgz
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