Dear list, dear Dr. Smyth

I am analyzing RNA-Seq data for the first time and I am confused with the value of common dispersion.
I have only two replicates between conditions (A1,A2: normal; B1,B2: oxidative stress)
and the value of common dispersion is

> d2<-estimateCommonDisp(d2)
> d2$common.dispersion
[1] 0.01859112
As far as I understand it is too low, is it?

In the User Guide  it is written that
'a common dispersion estimate of 0.2 means that there is a lot more variability in the data that can be accounted for by the Poisson model'

My estimate is much lower. Does it mean that I have to use Poisson model instead of NB?
If I have to use Poisson model, is it possible to do with edgeR package?

I would appreciate your advices!
Best regards
Galina

> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252

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

other attached packages:
[1] edgeR_2.6.0         limma_3.12.0        BiocInstaller_1.4.3

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