Could someone tell me the best way of normalizing RNA-seq data in order to make a comparison between several samples ?
Claus Weinholdt
Hi
if you just want compare a gene between samples then the DESeq or edgeR normalization for sample size should be fine.
if you also want compare gene X of sample A with gene Y of sample B then you better use the RPKM (FPKM) normalization
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Sindre Lee
Hi!
I know its common to just run with the default, but I would suggest box plotting your samples to compare distributions with different normalisation approaches.
This one quick way I do it (in edgeR and as example):
x2 is the DGEList object
# Here I use TMM normalisation (between samples) as an example:
tmm
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