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Old 06-15-2015, 11:14 PM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

If you really wanted to, you could convert the counts to RPKM or FPKM, though you shouldn't do statistics on those.

Alternatives to DESeq2 include edgeR and limma/voom, both of which will accept the same counts. DESeq2 doesn't account for gene length because it's constant between group. If you have a gene length bias between samples that's confounding things then look at the CQN package.
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