PAA (version 1.7.1)

batchAdjust: Adjust microarray data for batch effects.

Description

Adjusts EListRaw or EList data for batch/lot effects.

Usage

batchAdjust(elist=NULL, log=NULL)

Arguments

elist

EList or EListRaw object containing the data to be adjusted (mandatory).

log

logical indicating whether the data is in log scale (mandatory; note: if TRUE log2 scale is expected).

Value

An EListRaw or EList object with the adjusted data in log scale is returned.

Details

This is a wrapper to sva's function ComBat() for batch adjustment using the empirical Bayes approach. To use batchAdjust the targets information of the EList or EListRaw object must contain the columns "Batch" (containing batch/lot information for each particular array) and "Group" (containing experimental group information for each particular array).

References

The package sva by Jeffrey T. Leek et al. can be downloaded from Bioconductor (http://www.bioconductor.org/).

Johnson WE, Li C, and Rabinovic A (2007) Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8:118-27.

Examples

cwd <- system.file(package="PAA")
load(paste(cwd, "/extdata/Alzheimer.RData", sep=""))
elist <- elist[elist$genes$Block < 10,]
elist <- batchAdjust(elist=elist, log=FALSE)