batchAdjust: Adjust microarray data for batch effects.
In PAA: PAA (Protein Array Analyzer)

Description Usage Arguments Details Value Note Author(s) References Examples

Adjusts EListRaw or EList data for batch/lot effects.

1	batchAdjust(elist=NULL, log=NULL)

`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).

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).

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

The targets information of the EListRaw or EList object must contain the columns "Batch" and "Group".

Michael Turewicz, michael.turewicz@rub.de

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.

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