[BioC] Interspecies differential expression of orthologs with Edger

Gordon K Smyth smyth at wehi.EDU.AU
Wed Sep 3 01:08:44 CEST 2014

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

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