#library(preprocessCore)
#' @export
quantileNorm = function(whichFile,outFile=NULL){
if (is.character(whichFile)){
allDataPre = ogbox::read.exp(whichFile)
} else{
allDataPre = whichFile
}
list[geneData,exprData]= sepExpr(allDataPre)
newExprData = preprocessCore::normalize.quantiles(as.matrix(exprData))
# boxplot(newExprData)
newExprData = as.data.frame(newExprData)
colnames(newExprData) = colnames(exprData)
newAllData = cbind(geneData, newExprData)
if(is.character(outFile)){
write.csv(newAllData, file = outFile, row.names=FALSE)
}
invisible(newAllData)
}
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