[BioC] bayseq pair data

[alice [guest]]

I would like to run a paired baySeq analysis containing 11 pairs (primary vs. recurrent), so a total of 22 samples.  I am unsure of how to specify the groups and replicates parameters in the "pairedData" class.  There is no other grouping parameter.  They are all cases.  

thanks
alice

 -- output of sessionInfo(): 

R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics   grDevices utils     datasets methods   base

other attached packages:
[1] edgeR_3.0.8 limma_3.14.4  baySeq_1.12.0

loaded via a namespace (and not attached):
[1] tools_2.15.0

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