[BioC] Interspecies differential expression of orthologs with Edger

[assaf www]

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
>
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