[BioC] Interspecies differential expression of orthologs with Edger

assaf www assafwww at gmail.com
Mon Sep 8 22:41:39 CEST 2014

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,

On Mon, Sep 8, 2014 at 6:33 PM, Steve Lianoglou <lianoglou.steve at gene.com>

> 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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