[BioC] non-integer counts for edgeR

Gordon K Smyth smyth at wehi.EDU.AU
Wed May 23 09:33:08 CEST 2012

Hi Tim,

We have a few RNA-seq related papers in the pipeline, of which the voom 
paper is one.  We're investing a lot of time into trying to push edgeR and 
voom both along a similar pathway, to get the best use out of both.

Everyone in my lab would be happier if I didn't answer Bioconductor 
questions, because I'd get to their draft papers more quickly, and the 
voom one in particular ...


Professor Gordon K Smyth,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
smyth at wehi.edu.au

On Tue, 22 May 2012, Tim Triche, Jr. wrote:

> Hi Dr. Smyth,
> Will you be writing / have you already written a paper summarizing what
> voom() does and how?
> My understanding of voom() comes from
> http://statsandgenomes.wordpress.com/2011/11/23/bioinformatics-seminar-professor-gordon-smyth-variance-models-for-rna-seq/wherein
> it appears to be the current best general-purpose tool for treating
> RNAseq data as if it were microarray data.  This would seem to bring up
> issues with rare transcripts and the estimation of their abundance, which
> is why I ask about a writeup.
> Thanks as always for your patient explanations and high standards of work.
> --t
> On Tue, May 22, 2012 at 6:42 PM, Gordon K Smyth <smyth at wehi.edu.au> wrote:
>> 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
>> Gordon
>>  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
> -- 
> *A model is a lie that helps you see the truth.*
> *
> *
> Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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