batchCorrection: Batch correction for microarray data

In aroneklund/bias: Visualize, Quantify, and Correct Technical Bias in Microarray Data

Description

Removes batch differences from an expression matrix.

Usage

  batchCorrection(x, b)

Arguments

x	An ExpressionSet object, or a matrix.
b	A vector indicating batch membership for each column/sample in x.

Details

The idea is to correct for “batch-effect” systematic bias caused by inconsistent sample processing. In this context a “batch” may include groups of samples that were processed together, or scanned on the same date, etc.

This function adjusts each row (gene) of the expression matrix independently: For each row, a constant is added to all measurements within a batch, such that the mean within each batch is equal to the mean of the entire row.

Value

Either an ExpressionSet or a matrix (corresponding to x).

See Also

biasCorrection

Examples

  ## The Dilution data set was measured on two different scanners.
  library(affydata)
  data(Dilution)
  eset <- rma(Dilution)
  esetCorrected <- batchCorrection(eset, b = Dilution$scanner)

aroneklund/bias documentation built on May 10, 2019, 1:46 p.m.