Calculating differential expression from RPKM

Question

[Mukund]

I have a dataset (downloaded from GEO) that has expression levels in terms of RPKM. I understand that edgeR, DeSeq etc, use raw counts and not rpkm for differential expression calculation. Is there a way to find differential expression in case the raw counts are not available? Alternately, are there any easy ways to convert rpkm back to raw counts?

Thanks!

[karl.stamm]

Well it's reads per kilobase of exon per million mapped, so get those two numbers and multiply. It's not going to be clean or easy. Stop using RPKM.

Answer 1

[benformatics]

You could go backwards to counts from RPKM if you have the total number of mapped reads for each sample and the identity (and thus length) of all the genes/transcripts.