sva
function can be used to estimate artifacts from microarray data
the svaseq
function can be used to estimate artifacts from count-based
RNA-sequencing (and other sequencing) data. The ComBat
function can be
used to remove known batch effecs from microarray data. The fsva
function
can be used to remove batch effects for prediction problems.This function is the implementation of the iteratively re-weighted least squares
approach for estimating surrogate variables. As a by product, this function
produces estimates of the probability of being an empirical control. See the function
empirical.controls
for a direct estimate of the empirical controls.
sva(dat, mod, mod0 = NULL, n.sv = NULL, controls = NULL, method = c("irw", "two-step", "supervised"), vfilter = NULL, B = 5, numSVmethod = "be")
browseVignettes("sva")
in the R prompt.
For sva: Leek JT and Storey JD. (2008) A general framework for multiple testing dependence. Proceedings of the National Academy of Sciences , 105: 18718-18723.
For sva: Leek JT and Storey JD. (2007) Capturing heterogeneity in gene expression studies by `Surrogate Variable Analysis'. PLoS Genetics, 3: e161.
For Combat: Johnson WE, Li C, Rabinovic A (2007) Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics, 8 (1), 118-127
For svaseq: Leek JT (2014) svaseq: removing batch and other artifacts from count-based sequencing data. bioRxiv doi: TBD
For fsva: Parker HS, Bravo HC, Leek JT (2013) Removing batch effects for prediction problems with frozen surrogate variable analysis arXiv:1301.3947
For psva: Parker HS, Leek JT, Favorov AV, Considine M, Xia X, Chavan S, Chung CH, Fertig EJ (2014) Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction Bioinformatics doi: 10.1093/bioinformatics/btu375