[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
Gordon
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