sva: Surrogate Variable Analysis

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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).

Author
Jeffrey T. Leek <jtleek@gmail.com>, W. Evan Johnson <wej@bu.edu>, Hilary S. Parker <hiparker@jhsph.edu>, Elana J. Fertig <ejfertig@jhmi.edu>, Andrew E. Jaffe <ajaffe@jhsph.edu>, John D. Storey <jstorey@princeton.edu>
Date of publication
None
Maintainer
Jeffrey T. Leek <jtleek@gmail.com>, John D. Storey <jstorey@princeton.edu>, W. Evan Johnson <wej@bu.edu>
License
Artistic-2.0
Version
3.22.0

View on Bioconductor

Man pages

ComBat
Adjust for batch effects using an empirical Bayes framework
empirical.controls
A function for estimating the probability that each gene is...
f.pvalue
A function for quickly calculating f statistic p-values for...
fstats
A function for quickly calculating f statistics for use in...
fsva
A function for performing frozen surrogate variable analysis...
irwsva.build
A function for estimating surrogate variables by estimating...
num.sv
A function for calculating the number of surrogate variables...
psva
A function for estimating surrogate variables with the two...
ssva
A function for estimating surrogate variables using a...
sva
sva: a package for removing artifacts from microarray and...
sva.check
A function for post-hoc checking of an sva object to check...
svaseq
A function for estimating surrogate variables for count based...
twostepsva.build
A function for estimating surrogate variables with the two...

Files in this package

sva/DESCRIPTION
sva/NAMESPACE
sva/R
sva/R/ComBat.R
sva/R/empirical.controls.R
sva/R/f.pvalue.R
sva/R/fstats.R
sva/R/fsva.R
sva/R/helper.R
sva/R/irwsva.build.R
sva/R/num.sv.R
sva/R/psva.R
sva/R/ssva.R
sva/R/sva-package.R
sva/R/sva.R
sva/R/sva.check.R
sva/R/svaseq.R
sva/R/twostepsva.build.R
sva/build
sva/build/vignette.rds
sva/inst
sva/inst/doc
sva/inst/doc/sva.R
sva/inst/doc/sva.Rnw
sva/inst/doc/sva.pdf
sva/man
sva/man/ComBat.Rd
sva/man/empirical.controls.Rd
sva/man/f.pvalue.Rd
sva/man/fstats.Rd
sva/man/fsva.Rd
sva/man/irwsva.build.Rd
sva/man/num.sv.Rd
sva/man/psva.Rd
sva/man/ssva.Rd
sva/man/sva.Rd
sva/man/sva.check.Rd
sva/man/svaseq.Rd
sva/man/twostepsva.build.Rd
sva/src
sva/src/sva.c
sva/tests
sva/tests/testthat
sva/tests/testthat.R
sva/tests/testthat/test_combat_bladderbatch.R
sva/tests/testthat/test_combat_errors.R
sva/tests/testthat/test_combat_sim.R
sva/vignettes
sva/vignettes/sva.Rnw
sva/vignettes/sva.bib