sva v3.20.0

by Jeffrey T Leek

Surrogate Variable Analysis

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 three ways: (1) identifying and estimating surrogate variables for unknown sources of variation in high-throughput experiments (Leek and Storey 2007 PLoS Genetics,2008 PNAS), (2) directly removing known batch effects using ComBat (Johnson et al. 2007 Biostatistics) and (3) removing batch effects with known control probes (Leek 2014 biorXiv). 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).

Functions in sva

Name Description
fsva A function for performing frozen surrogate variable analysis as proposed in Parker, Corrada Bravo and Leek 2013
twostepsva.build A function for estimating surrogate variables with the two step approach of Leek and Storey 2007
empirical.controls A function for estimating the probability that each gene is an empirical control
f.pvalue A function for quickly calculating f statistic p-values for use in sva
svaseq A function for estimating surrogate variables for count based RNA-seq data.
psva A function for estimating surrogate variables with the two step approach of Leek and Storey 2007
sva sva: a package for removing artifacts from microarray and sequencing data
ssva A function for estimating surrogate variables using a supervised approach
ComBat Adjust for batch effects using an empirical Bayes framework
fstats A function for quickly calculating f statistics for use in sva
num.sv A function for calculating the number of surrogate variables to estimate in a model
sva.check A function for post-hoc checking of an sva object to check for degenerate cases.
irwsva.build A function for estimating surrogate variables by estimating empirical control probes
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License Artistic-2.0
biocViews Microarray, StatisticalMethod, Preprocessing, MultipleComparison, Sequencing, RNASeq, BatchEffect, Normalization

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