From 22496b5f644dea1ba9b4e9a8dd7c9c8463727884 Mon Sep 17 00:00:00 2001 From: Jens Preussner Date: Wed, 31 Aug 2016 11:50:06 +0200 Subject: [PATCH] Added qn.bmiq normalization --- src/normalizeAndCreateTables.R | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/src/normalizeAndCreateTables.R b/src/normalizeAndCreateTables.R index a33bbd8..9a8e977 100755 --- a/src/normalizeAndCreateTables.R +++ b/src/normalizeAndCreateTables.R @@ -49,3 +49,15 @@ if(normalization == "quantile") { write.table(getM(mSet)[-failed_probes,], file = paste(targetDir, "mValues_quantile.txt", sep="/"), quote = F, sep = "\t", row.names = T, col.names = T) write.table(getBeta(mSet)[-failed_probes,], file = paste(targetDir, "betaValues_qunatile.txt", sep="/"), quote = F, sep = "\t", row.names = T, col.names = T) } + +if(normalization == "qn.bmiq") { + mSet = preprocessQuantile(rgSet, fixOutliers=fixOutliers, removeBadSamples=removeBadSamples, badSampleCutoff=badSampleCutoff) + betas = getBeta(mSet)[-failed_probes,] + design = ifelse(rownames(betas) %in% getProbeInfo(rgSet, type="I")$Name, 1, 2) + bnorm = lapply(1:ncol(betas), function(i) BMIQ(betas[,i],design=design)$all) + betaValues = do.call("cbind", bnorm) + colnames(betaValues) = colnames(betas) + mValues = apply(betaValues, 2, logit2) + write.table(mValues, file=paste(targetDir, "mValues_qn.bmiq.txt", sep="/"), quote = F, sep = "\t", row.names = T, col.names = T) + write.table(betaValues, file=paste(targetDir, "betaValues_qn.bmiq.txt", sep="/"), quote = F, sep = "\t", row.names = T, col.names = T) +}