Question: rsem matrix to DESeq2
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gravatar for Folder40g
9 weeks ago by
Folder40g110
Folder40g110 wrote:

I know that I can pass the gene-level rsem matrix to limma and work with it.

But can I use it in DESeq?

I've a rsem matrix from firebrowse, gene-level ~20000 rows. DESeq requires raw counts, and as I only have the matrix with samples/gene I can't use tximport().

Thanks

rsem • 190 views
ADD COMMENTlink modified 9 weeks ago by Kevin Blighe25k • written 9 weeks ago by Folder40g110
1
gravatar for Kevin Blighe
9 weeks ago by
Kevin Blighe25k
USA / Europe / Brazil
Kevin Blighe25k wrote:

You can use these with DESeq2 if you just round the numbers to whole integers and then input to DESeq2 with DESeqDataSetFromMatrix(). It is not ideal and using tximport would be preferred, as it does some adjustments for transcript length and transcript isoform abundances.

If you don't take my word, then take that of the DESeq2 developer: DESeq2 Following RSEM

Please be sure that you definitively have the un-normalised FireBrowse counts, though.

Kevin

ADD COMMENTlink written 9 weeks ago by Kevin Blighe25k
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