normalize.ExpressionSet.mc: mean centering normalization

In ShixiangWang/arrayConnector: Connect high throughput Array data from different platforms

Description

Performs mean centering on the supplied ExpressionSet object.

Usage

normalize.ExpressionSet.mc(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

Tibshirani R, Hastie T, Narasimhan B, Chu G: Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proceedings of the National Academy of Sciences of the United States of America 2002, 99:6567-6572.

See Also

virtualArrayExpressionSets

Examples

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

ShixiangWang/arrayConnector documentation built on May 14, 2019, 6:02 a.m.