[BioC] Deseq for pairwise comparison among many pairs

[Feng, Shihai]

I have two  questions related to how to use Deseq.

1) I have total three sample treatments. I am doing pairwise comparison between treatments. I am wondering what sample pool I should use to calcualte SizeFactors and Dispersion.   Should I  use only  the two treatments data that I use in the subsequent nbinomTest  step or use all my three sample treatments to calculate SizeFactors and Dispersion.

2) My sample is bacterial that includes chromosome and plasmids, should I study them separately or together ? More specifically,  should I run your deseq pipeline independently on chromosome and plasmid or should I combine  chromosome and plasmid data first then run your deseq pipeline.

thanks,
shihai