I'm interested in analyze some RNA-Seq data from Encode. They have posted a gene quantification file for each sample from RSEM. My understanding is that I can pass the expected counts to voom and then limma even though raw counts is more ideal. I just wanted to check that this is correct?

Thanks

Take a look at tximport.

If you are working with RSEM gene-level expected counts, then you can just pass them to limma as if they were counts. That's what we do.

If you work with RSEM transcript level summaries, then perhaps tximport can do some finesse. I haven't tried that yet.