[BioC] non-integer counts for edgeR

Gordon K Smyth smyth at wehi.EDU.AU
Wed May 23 03:42:21 CEST 2012

Dear Mete,

No, you cannot use non-integer counts with edgeR.

If you must use non-integer counts, please use the voom() function in the 
limma package instead.  This will do an analysis that is not too different 
from edgeR, just a little less powerful, and is not bothered by 
non-integer values.

Best wishes

> Date: Mon, 21 May 2012 12:24:43 -0700
> From: Mete Civelek <mcivelek at mednet.ucla.edu>
> To: <bioconductor at r-project.org>
> Subject: [BioC] non-integer counts for edgeR
> Dear All,
> I am analyzing microRNAseq data with edgeR. Because some of the reads map to
> multiple locations, I weighed the counts based on the number of genomic
> locations that a read maps. For example, if a read maps to 3 locations, each
> location gets a count of 1/3. Of course, this means that the read counts for
> some miRNAs in some samples are not integers. Is it possible to use these
> counts to do differential expression analysis with a quantitative trait in
> edgeR? My understanding is "no" but I thought someone can suggest a
> solution.
> Thank you for your help.
> Best Regards,
> Mete

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