Surrogate Variable Analysis

Documentation for package ‘sva’ version 3.26.0

sva-package	sva: a package for removing artifacts from microarray and sequencing data
ComBat	Adjust for batch effects using an empirical Bayes framework
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
fstats	A function for quickly calculating f statistics for use in sva
fsva	A function for performing frozen surrogate variable analysis as proposed in Parker, Corrada Bravo and Leek 2013
irwsva.build	A function for estimating surrogate variables by estimating empirical control probes
num.sv	A function for calculating the number of surrogate variables to estimate in a model
psva	A function for estimating surrogate variables with the two step approach of Leek and Storey 2007
qsva	A function for computing quality surrogate variables (qSVs)
read.degradation.matrix	A function for reading in coverage data from degradation-susceptible regions
ssva	A function for estimating surrogate variables using a supervised approach
sva	sva: a package for removing artifacts from microarray and sequencing data
sva.check	A function for post-hoc checking of an sva object to check for degenerate cases.
svaseq	A function for estimating surrogate variables for count based RNA-seq data.
twostepsva.build	A function for estimating surrogate variables with the two step approach of Leek and Storey 2007