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!
Michael,
Thanks for your response. Could you please tell me why transcript-level counting is non-integer?
Thanks, Hadi
Please do not ask unrelated questions in old threads, and please use the
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button, not the answer field. It is not integer because it is abundance estimates, not counts.tximport
will then produce gene level counts.