Question

How to import RSEM results to DESeq2 for differential analysis

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7.0 years ago

402374688 ▴ 30

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 • 6.1k views

ADD COMMENT • link updated 4.7 years ago by hosseini • 0 • written 7.0 years ago by 402374688 ▴ 30

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Michael,

Thanks for your response. Could you please tell me why transcript-level counting is non-integer?

Thanks, Hadi

ADD REPLY • link 4.7 years ago by hosseini • 0

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Please do not ask unrelated questions in old threads, and please use the ADD COMMENT button, not the answer field. It is not integer because it is abundance estimates, not counts. tximport will then produce gene level counts.

ADD REPLY • link 4.7 years ago by ATpoint 85k

ATpoint · Answer 1 · 2017-12-11

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).

Edit 4.3.2020 by ATpoint since this thread gets a lot of views:

The manual contains example code on how to use RSEM output with tximport, which can then be processed with DESeqDataSetFromTximport()