[BioC] Interspecies differential expression of orthologs with Edger

[Sean Davis]

On Sun, Sep 7, 2014 at 3:32 PM, assaf www <assafwww at gmail.com> wrote:

> Dear Gordon
>
> I am aware of the limitations of the corss-species inference -
> Still , it is critical for me to minimize false positives, before the
> real-time PCR validation stage.
>
> Just trying to understand some other things, that may, or may not, be
> related to the corss-species issue:
> Edger manual says that any kind of "genomic feature" may be used,
> but can "genomic feature" also be defined as 'groups of genes' ?
> I mean, can it be correct to try Edger after summing up the counts of genes
> belonging to specific categories
> (e.g. gene families) ? so instead of having 12,000 genes I end up with, say
> 2,000 gene groups ?
> this can also be good for the FDR, etc.
>

Hi, Assaf.

edgeR and other related tools will happily use counts from arbitrary
genomic features and have been applied to data such as DNAse-Seq and
ChIP-Seq.  I'm not sure how doing so will "be good for the FDR", but I may
misunderstand your point.

Sean



>
> Thanks a lot, all the Best,
> Assaf
>
> On Sun, Sep 7, 2014 at 4:11 AM, Gordon K Smyth <smyth at wehi.edu.au> wrote:
>
> > Dear Assaf,
> >
> > You are getting the sort of results that I would expect you to get when
> > you try to compare two RNA sources that are very different.
> >
> > The diagonal lines in the MA plot are simply a result of having low
> counts
> > (0,1,2 etc) in one species and high counts in the other for the same
> genes.
> >
> > When you compare different species, I'd intuitively expect almost every
> > gene to be differentially expressed to some degree.  So I'm not surprised
> > that a large proportion of genes are assesssed as DE.
> >
> > That's about as much help as I can give you.  I can't give advice that
> > would allow you to get the same sort of results as you might be used to,
> > because comparing different species isn't a normal thing to do.
> >
> > Best wishes
> > Gordon
> >
> >
> >  Date: Fri, 5 Sep 2014 23:22:28 +0300
> >> From: assaf www <assafwww at gmail.com>
> >> To: Gordon K Smyth <smyth at wehi.edu.au>
> >> Cc: Bioconductor mailing list <bioconductor at r-project.org>
> >> Subject: Re: [BioC] Interspecies differential expression of orthologs
> >>         with    Edger
> >>
> >> Thanks Gordon,
> >>
> >> To summarize the results I got on the cross-species data, after
> embedding
> >> the length-effect to the GLM offset matrix, as in the code you sent,
> >> please
> >> see the attached MA plot:
> >>
> >> 1) for >5 and <-5 log fold change, genes' logFC is positively correlated
> >> with mean log CPM, something I haven?t seen before in Edger standard
> runs.
> >> 2) most genes with fold change around > 1.3, or < -1.3, are significant,
> >> which looks to me too ?liberal?. Please note that each group contains 6
> >> true biological replicates (variance within each group is large) .
> >>
> >> The first problem worries me most, any idea is very welcomed.
> >>
> >> Many thanks,
> >> Assaf
> >>
> >>
> >>
> >> On Wed, Sep 3, 2014 at 2:08 AM, Gordon K Smyth <smyth at wehi.edu.au>
> wrote:
> >>
> >>
> >>> On Tue, 2 Sep 2014, assaf www wrote:
> >>>
> >>>  Does Edger DE analysis is built on the assumption that most genes are
> >>> not
> >>>
> >>>> differentially expressed, and that only a small portion of them do
> (say
> >>>> <20%)  ?
> >>>>
> >>>>
> >>> Only the calcNormFactors() step of edgeR makes any assumption of this
> >>> sort. calcNormFactors assumes that either that most genes are not DE or
> >>> that the DE is reasonably symmetric.
> >>>
> >>>  I mean, in cross-species studies, or when comparing different tissues
> of
> >>>
> >>>> the same organism, if this assumption doesn't hold, should it be a
> >>>> serious
> >>>> concern ?
> >>>>
> >>>>
> >>> In a cross-species comparison there will be many DE genes, but some
> will
> >>> be up and some will be down.  The DE will not be all in one direction,
> I
> >>> would guess that normalization will not be a serious concern.
> >>>
> >>> Of all the concerns with cross-species comparisons, this seems to me to
> >>> be
> >>> far from the most serious.
> >>>
> >>> Best wishes
> >>> Gordon
> >>>
> >>>  -------------- next part --------------
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> >>
> >> ------------------------------
> >>
> >
> > ______________________________________________________________________
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