The sva package for removing batch effects and other unwanted variation in high-throughput experiments

JT Leek, WE Johnson, HS Parker, AE Jaffe… - …, 2012 - academic.oup.com
Bioinformatics, 2012academic.oup.com
Heterogeneity and latent variables are now widely recognized as major sources of bias and
variability in high-throughput experiments. The most well-known source of latent variation in
genomic experiments are batch effects—when samples are processed on different days, in
different groups or by different people. However, there are also a large number of other
variables that may have a major impact on high-throughput measurements. Here we
describe the sva package for identifying, estimating and removing unwanted sources of …
Abstract
Summary: Heterogeneity and latent variables are now widely recognized as major sources of bias and variability in high-throughput experiments. The most well-known source of latent variation in genomic experiments are batch effects—when samples are processed on different days, in different groups or by different people. However, there are also a large number of other variables that may have a major impact on high-throughput measurements. Here we describe the sva package for identifying, estimating and removing unwanted sources of variation in high-throughput experiments. The sva package supports surrogate variable estimation with the sva function, direct adjustment for known batch effects with the ComBat function and adjustment for batch and latent variables in prediction problems with the fsva function.
Availability: The R package sva is freely available from http://www.bioconductor.org.
Contact:  jleek@jhsph.edu
Supplementary information:  Supplementary data are available at Bioinformatics online.
Oxford University Press