quantileNormalise {beadarray}R Documentation

Quantile Normalisation for BeadLevelList objects

Description

Normalizes expression intensities so that the intensities or log-ratios have similar distributions across a series of arrays.

Function is based on the 'normalizeBetweenArrays' function in 'limma'

Usage

quantileNormalise(BLData, arrays=1:length(BLData$R[1,]))

Arguments

BLData can be either an BeadLevelList or BeadSummaryList object
arrays choose a subset of arrays to normalise

Details

Quantile normalization was proposed by Bolstad et al (2003) for Affymetrix-style single-channel arrays and by Yang and Thorne (2003) for two-color cDNA arrays. 'method="quantile"' ensures that the intensities have the same empirical distribution across arrays and across channels.

Value

Produces an BeadLevelList or BeadSummaryList (depending on input type) containing normalised intensity values.

Author(s)

Mark Dunning

See Also

qsplineNormalise medianNormalise

Examples


data(BSData)

BSData.q = quantileNormalise(BSData)

#All distributions are fixed to be the same

boxplot(BSData.q$R~col(BSData.q$R))


[Package beadarray version 1.0.0 Index]