[BioC] DESeq - non-differential expression

[Thomas J Hardcastle]

Dear Christophe,

With a classical statistical approach, you are correct that there is a 
difficulty in attributing p-values to non-differential expression. If we 
adopt a Bayesian approach, however, we can calculate the posterior 
likelihood of non-differential expression; you may therefore want to 
take a look at the 'baySeq' package, which can make such inferences.

Best regards,

Tom Hardcastle

-- 
Dr. Thomas J. Hardcastle

Department of Plant Sciences
University of Cambridge
Downing Street
Cambridge, CB2 3EA
United Kingdom


>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 14 Apr 2011 13:08:47 +0200
> From: Christophe Antoniewski <christophe.antoniewski at pasteur.fr>
> To: bioconductor at r-project.org
> Subject: [BioC] DESeq - non-differential expression
> Message-ID: <FF206021-EBCD-46CD-909A-B9A45416E7B4 at pasteur.fr>
> Content-Type: text/plain
>
> 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
> Cell phone:  33 6 68 60 51 50
> Fax:  33 1 40 61 36 27
> Lab Web site: http://drosophile.org
> Post-Doc Position Available
>
>