beadarray (version 2.22.2)

medianNormalise: Median normalise data in a matrix

Description

Normalises expression intensities so that the intensities or log-ratios have equal median values across a series of arrays (columns).

Usage

medianNormalise(exprs, log=TRUE)

Arguments

exprs

a matrix of expression values

log

if TRUE then do a log2 transformation prior to normalising

Value

Produces a matrix of normalised intensity values (on the log2 scale by default) with the same dimensions as exprs.

Details

Normalisation is intended to remove from the expression measures any systematic trends which arise from the microarray technology rather than from differences between the probes or between the target RNA samples hybridized to the arrays.

For median normalisation, the intensity for each gene is adjusted by subtracting the median of all genes on the array and then adding the median across all arrays. The effect is that each array then has the same median value.

Examples

if(require(beadarrayExampleData)){

data(exampleSummaryData)

exampleSummaryData.log2 <- channel(exampleSummaryData,"G")

exampleSummaryData.med = assayDataElementReplace(exampleSummaryData.log2, "exprs", medianNormalise(exprs(exampleSummaryData.log2)))

}