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Calculating differential expression from RPKM

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!

rna-seq edger deseq r
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updated by benformatics benformatics • written by Mukund • Mukund

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.

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updated by Ram Ram • written by karl.stamm karl.stamm

2 answers

you can use limma with the voom transformation

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updated by Ram Ram • written by TriS TriS

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.

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written by benformatics benformatics

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