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@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@mednet.ucla.edu>
>> To: <bioconductor@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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