[BioC] DESeq - non-differential expression

[Wolfgang Huber]

Dear Christophe

if you think about a set of possible worlds that are indexed by the 
parameter epsilon, and for which qi(A)=qi(B)+epsilon is true, then it 
would be difficult to construct a test that keeps its type I error 
(probability of false rejection) for all (nulls) epsilon!=0 but has any 
power for the (alternative) epsilon=0.

Absence of evidence is obviously not the same as evidence of absence, 
but I think using the failure to reject the null hypothesis qi(A)=qi(B) 
as an absence of evidence for differential expression -as you suggest- 
is one of the better things you can do here.

	Wolfgang


Il Apr/14/11 1:08 PM, Christophe Antoniewski ha scritto:
> Hi,
>
> We are routinely using the DESeq package to identify miRNA differentially expressed in small RNA sequencing datasets from 2 biological conditions (A and B).
> Recently, we got interested in miRNA species that do *not* change.
>
> In a quick approach, we reasoned that miRNAs that do not change are those that are not significantly differentially expressed (Yes,we are big brain).
> But then I realized that because the H0 hypothesis upon DESeq usage is qi(A)=qi(B) it is not really possible to attribute a p-value to a "non-differential" expression
> I suspect (I am not a statistician) that to do this we should revert the H0 hypothesis in the DESeq procedure, something like qi(A) != qi(B).
>
> Does it make sense, and if so, is there any possibility to do this with DESeq ?
>
> Thanks for the help
>
>
> Christophe Antoniewski
>
> Drosophila Genetics and Epigenetics
> Institut Pasteur
> 25 rue du Dr Roux
> 75724 Paris cedex 15
> Lab Tel:  33 1 44 38 93 35
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber