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Old 12-05-2013, 01:18 AM   #3
Simon Anders
Senior Member
Location: Heidelberg, Germany

Join Date: Feb 2010
Posts: 994

Are you sure that you used counts per gene, and not counts per transcript, as input? RSEM outputs the latter by default, but these are unsuitable (even in principle) for downstream analysis for differential expression testing. (If you don't know why, see my earlier posts on the subject.)
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