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
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