[BioC] Interspecies differential expression of orthologs with Edger

Gordon K Smyth smyth at wehi.EDU.AU
Tue Sep 9 01:47:29 CEST 2014

Dear Assaf,

Please type


to see the roast gene set test that Steve was referring to.  It tests 
whether a set of genes is differentially expressed as a group.


On Mon, 8 Sep 2014, assaf www wrote:

> Hi Steve
> I will look into limma::voom (was not aware of this approach).
> Do you mean GO enrichment (e.g., David/Go-seq/etc), is so then no, its not
> what I mean.
> I specifically would like to ask if Edger (or similar tools) could give
> reasonable DE estimation by comparing the sum of counts of groups of genes
> (instead single genes).
> This is a completely different thing - it may possibly allow working-around
> the issue of paralogy-orthology when performing cross-species DE analysis,
> and may have multiple other advantages I believe (regardless of
> cross-species things).
> (Of course, in case it doesn't violate the basic assumptions of these DE
> analyzes, and can keep the data properly normalized - this is my question)
> thanks a lots for the suggestions, i will look into,
> Assaf
> On Mon, Sep 8, 2014 at 6:33 PM, Steve Lianoglou <lianoglou.steve at gene.com>
> wrote:
>> Hi,
>> On Mon, Sep 8, 2014 at 1:17 AM, assaf www <assafwww at gmail.com> wrote:
>>> Hi sean
>>> I guess I'm not clear, sorry.
>>> I mean that in principle it is possible to aggregate genes based on their
>>> membership in gene families (or any other criteria), and to compare the
>> sum
>>> of read counts per sample per groups of genes (usually it would be counts
>>> per sample per genes). What I would be interested to learn is if such
>>> comparison can be done in Edger.
>>> About FDR : In the above case, after grouping there are less multiple
>>> comparisons, and lower FDR.
>> Instead of grouping different genes into one "count feature," it's
>> sounds like keeping genes separate, but doing a gene set enrichment
>> analysis might be more like what you are looking for?
>> edgeR and limma::voom have these out of the box -- look at the camera
>> and roast functions for further info on that.
>> HTH,
>> -steve
>> --
>> Steve Lianoglou
>> Computational Biologist
>> Genentech

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