quantileNormalise {beadarray} | R Documentation |
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'
quantileNormalise(BLData, arrays=1:length(BLData$R[1,]))
BLData |
can be either an BeadLevelList or BeadSummaryList object |
arrays |
choose a subset of arrays to normalise |
Quantile normalization was proposed by Bolstad et al (2003) for Affymetrix-style single-channel arrays and by Yang and Thorne (2003) for two-color cDNA arrays. 'method="quantile"' ensures that the intensities have the same empirical distribution across arrays and across channels.
Produces an BeadLevelList or BeadSummaryList (depending on input type) containing normalised intensity values.
Mark Dunning
qsplineNormalise
medianNormalise
data(BSData) BSData.q = quantileNormalise(BSData) #All distributions are fixed to be the same boxplot(BSData.q$R~col(BSData.q$R))