[BioC] Interspecies differential expression of orthologs with Edger

Steve Lianoglou lianoglou.steve at gene.com
Mon Sep 8 17:33:24 CEST 2014


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.


Steve Lianoglou
Computational Biologist

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