[BioC] DEXSeq: subsetting ExonCountSet ?

[Yvan Wenger]

Hello everybody,

I have 11 libraries representing 6 different conditions (some are in
triplicates). Is there a simple way to test for differential
expression using DEXSeq between two libraries I actually choose?

For example, in the DESeq pacakge, we use the command res =
nbinomTest( cds, "untreated", "treated" ) which clearly specifies the
conditions between the two samples to test, but I do not see any
possibility to input the conditions I want in the DEXSeq function
testForDEU(). I would like to be able to use dispersions calculated
with all my conditions even if I test only condition pairs (like in
DESeq basically).

Many thanks for your help,

Yvan