ber (version 2.0)

ber: Batch Effects Removal

Description

The function ber removes batch effects from (microarray) data. This function uses information about the batches and the expression levels in the data.

Usage

ber(Y, b)

Arguments

Y

A matrix with $n$ rows and $g$ columns, where $n$ is the number of objects and $g$ is the number of variables. In the case of gene expression data, columns correspond to genes and rows to samples.

b

A vector of class factor with the element in position $i$ ($i=1,\ldots,n$) representing the batch from which observation $i$ belongs to.

Value

• A matrix of adjusted data with $n$ rows and $g$ columns.

References

M. Giordan (Submitted). An efficient two-stage procedure for removing batch effects in high dimensional data experiments.

See Also

berCov

Examples

library(golubEsets)
library(vsn)
data(Golub_Merge)
E<-exprs(vsn2(Golub_Merge))
batch<-Golub_Merge$Source
Eadj<-ber(t(E),batch)