Entering edit mode
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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