QC_EdgeR() boxplot of normalized counts

Hello, I have a question that is maybe more related to EdgeR than miARma. I noticed that the "normalized counts data boxplot" (and density & heatmaps) are generated with dgenorm$counts, e.g. :

#Normalization of the samples dgenorm<-calcNormFactors(dge,method=normethod) #Boxplot of the normalized samples boxplot(log2(dgenorm$counts), col=boxcol, main=paste("Boxplot of ", label , " normalized samples",sep=""), las=2, names=samplenames, ylab="log2(counts)", xlab="")

Aren't the raw (filtered) counts of dge left unchanged when applying calcNormFactors(), that is dgenorm$counts==dge$counts? calcNormFactors() only adds normalized factors in the form of object$samples$norm.factors to the DGElist dge object? If so, the only way to get "normalized" boxplots/density plots is to use cpm() or rpkm() on dgenorm ?

Regards, Guillaume Noell

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