medianNormalise {beadarray}R Documentation

Median Normalisation for BeadLevelList objects

Description

Normalizes expression intensities so that the intensities or log-ratios have equal median values across a series of arrays.

Usage

medianNormalise(BLData)

Arguments

BLData can be either an BeadLevelList object or an BeadSummaryList object.

Details

Normalization 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.

Value

Produces an BeadLevelList containing normalised intensity values. Values will be on the log2 scale

Author(s)

Mark Dunning

Examples


data(BLData)

BLData.med = medianNormalise(BLData)

#All distributions are fixed to have same median

boxplot(BLData.med$R~col(BLData.med$R))


[Package beadarray version 1.0.0 Index]