RSEM expected counts to limma-voom
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Jake ▴ 90
@jake-7236
Last seen 7 months ago
United States

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

limma voom rsem • 2.1k views
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Is the RSEM quantification by gene or by transcript?

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They have both. I was interested in the gene quantification.

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@james-w-macdonald-5106
Last seen 31 minutes ago
United States

Take a look at tximport.

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@gordon-smyth
Last seen 8 hours ago
WEHI, Melbourne, Australia

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.

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