Question: How to import RSEM results to DESeq2 for differential analysis
2
gravatar for 402374688
2.2 years ago by
40237468820
40237468820 wrote:

The results of RSEM are expected counts of transcripts and genes and they are not integer. DESeq2, however, need a matrix of integer as input. The manual of RSEM said the results of RSEM can be used by DESeq. So my question is how to import non-integer RSEM counts to DESeq2 for downstream differential analysis? Thank you!

rsem deseq2 • 1.6k views
ADD COMMENTlink modified 2.2 years ago by Michael Love1.9k • written 2.2 years ago by 40237468820
6
gravatar for Michael Love
2.2 years ago by
Michael Love1.9k
United States
Michael Love1.9k wrote:

You can use tximport to import RSEM quants and then DESeqDataSetFromTximport() in DESeq2. The development version of tximport allows importing transcript-level abundances as well (previously just gene-level).

ADD COMMENTlink written 2.2 years ago by Michael Love1.9k
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