normalize.ExpressionSet.gq: gene quantiles normalization

In virtualArray: Build virtual array from different microarray platforms

Description

Performs gene quantile normalization for cross-platform adjustments of microarray data. It is a modification of the median rank scores normalization.

Usage

normalize.ExpressionSet.gq(ExpressionSet = NULL, Batch = NULL, ...)

Arguments

ExpressionSet	An ExpressionSet object; if it contains a "Batch" column in its pData slot, this information can be used instead of the "Batch" parameter.
Batch	A character or numeric vector containing batch contribution of the samples. The order of the items should be the same as the samples (column) in the supplied ExpressionSet. Defining this parameter overrides the information of the pData slot.
...	Can be used to pass on parameters to underlying functions.

Details

Please see the references for details.

Value

An ExpressionSet object with adjusted expression matrix.

Author(s)

Andreas Heider

References

Xia XQ, McClelland M, Porwollik S, Song W, Cong X, Wang Y: WebArrayDB: cross-platform microarray data analysis and public data repository. Bioinformatics 2009, 25:2425-2429.

See Also

virtualArrayExpressionSets

Examples

# library(affydata)
# data(Dilution)
# Dilution <- rma(Dilution)
# normalize.ExpressionSet.gq(Dilution,Batch=c("A","B","A","B"))

virtualArray documentation built on Sept. 12, 2016, 6:10 a.m.