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Old 12-04-2013, 10:19 AM   #2
mmuurr
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Join Date: Oct 2013
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i don't have an answer, but essentially am curious about the same point.
i believe the TCGA Level 3 RNASeqv2 "unnormalized" data represents the 'raw' RSEM counts, and thus piping this input into edgeR would be fine... but perhaps i'm mistaken.
one spot where i've seen conflicting opinions is on how edgeR handles non-integer based counts, which will be the case with the RSEM output.

in a few test cases i've run, i haven't encountered any glaring errors, though i found a HUGE number of differentially expressed genes when comparing prostate cancer samples (both unmatched cases using exact tests and using a subset of matched cases using a GLM approach to handle the paired samples).
at an FDR threshold of 0.05 (using B-H correction), nearly half the genome qualified as differentially expressed, which -- at first glance -- seemed high to me.
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