Dear all,


Until now I was doing RNAseq DE analysis and to do that I understand that
normalization issues only matter inside samples, because one can assume the
length/content biases will cancel out when comparing same genes in different
samples.
Although, I'm now trying to compare correlation of different genes and so,
this biases should be taken into account - for this is there any better
method than RPKM?

My main doubt is if I should also take into acount the biases inside samples
and to do that is there any better approach then TMM by Robinson and Oshlack
[2010]?

Thank you all,
-- 
João Moura

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