I have been looking around for this in the already-asked questions, but I could not find it, so I am sorry, if this has been asked before.
I would like to use quantile normalization. What I am doing is looking at 2 datasets in which treated samples are compared with control samples. The commands I am using are as follows (using package voom):
initDGE <- DGEList(counts, groups)
quant <- voom(initDGE, design, normalize.method="quantile")
quantNorm <- quant$E
I know, that the 'quantNorm' object holds the normalized data.
But, does quantile normalization the way I do it here take into account the library size? So, does it take into account the library size to correct for that? I have a feeling, the way quantile normalization should work, it does not really matter whether it does. Is that correct?
Thank you for your help