batchAdjust: Adjust microarray data for batch effects.

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

View source: R/PAA.r

Description

Adjusts EListRaw or EList data for batch/lot effects.

Usage

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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).

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).

Value

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

Note

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

Author(s)

Michael Turewicz, michael.turewicz@rub.de

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

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

PAA documentation built on Nov. 8, 2020, 8:30 p.m.