Re: Interspecies differential expression of orthologs with Edger

thanks for the ideas,
you probably mean this method ?
http://www.broadinstitute.org/gsea/index.jsp
also will check if DexSeq can help here

Assaf

On Mon, Sep 8, 2014 at 11:55 PM, Steve Lianoglou <lianoglou.steve-RuTDbSqP/[email protected]>
wrote:

> Hi,
>
> On Mon, Sep 8, 2014 at 1:41 PM, assaf www <[email protected]> wrote:
> > Hi Steve
> >
> > I will look into limma::voom (was not aware of this approach).
>
> This is "just" another approach to do differential expression analysis
> with rna-seq data -- ie. one could use edgeR, DESeq2, limma::voom,
> etc. to do "standard" differential expression (count) testing.
>
> > Do you mean GO enrichment (e.g., David/Go-seq/etc), is so then no, its
> not
> > what I mean.
>
> No, I do not mean GO enrichment, I really meant "gene set enrichment
> analysis", it's "a thing" ... look at the help and references listed
> under ?camera and ?roast, I thought your motivation to group
> "features" together was to do something along those lines but from
> what you say below, it seems not (?)
>
> > 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).
>
> It's not clear to me what "reasonable" means in this case, to be honest.
>
> > 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)
>
> Without getting too involved here, my gut feeling is that going about
> things in this way is making things worse ... not better.
>
> I'm not sure where to start pointing you for some help, and this might
> be entirely unrelated (but I'll let you figure that one out ;-), but
> maybe you can take a look at the paper written by the DEXSeq folks:
>
> Drift and conservation of differential exon usage across tissues in
> primate species
> http://www.pnas.org/content/110/38/15377.short
>
> I admit that this isn't directly doing what you are doing, but perhaps
> they touch upon some issues that might be of help to you ... to be
> honest, however, I haven't given it a good read through, even though
> it has been on my "readme" list for sometime (over a year,
> apparently!).
>
> -steve
>
> --
> Steve Lianoglou
> Computational Biologist
> Genentech
>

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