Hi all

 

I’m quite new to illumina analysis. I read non-normalised data and did a
quantile normalisation. 

library(beadarray)

BSData <- readBeadSummaryData(targets=NULL, header=T, sep="\t",path=
NULL,

                                   columns = list(ProbeID = "TargetID",

                                     AvgSig = "AVG_Signal", Nobeads =
"Avg_NBEADS",

                                     Detection="Detection",
BeadStDev="BEAD_STDEV"),

                                   other.columns = NULL, skip=7)

BSData.quantile = normaliseIllumina(BSData, method = "quantile")

normalised <- exprs(BSData.quantile)

write.csv(file="normalised.csv", normalised)

 

Is quantile normalisation good enough? What normalisation methods are
considered good for illumina data? Your feedback will be much
appreciated. 

 

Thanks heaps

Yogi

 

 



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