[BioC] which dispersion to choose

[Ruprecht Kathrin]

Dear all,

I'd like to use edgeR to find differently expressed genes in my RNAseq data. My question is which dispersion I should use.
In a forum I read that moderate tagwise dispersion ranks more highly the DE genes which are consistent in their group - which is what I am looking for.
How can I achive "moderate" tagwise dispersion or could I use trended dispersion instead?

My data consists of 18 libraries with 3 treatments (6 libraries each). In these treatments I have 2 groups of 3 libraries each which are not exactly replicates but should behave similarly.
I want to test mainly for differences between the groups in each treatment.

Thanks for your Help!
Kind Regards

Kathrin Ruprecht
Master student 
Plant ecological genetics
ETH Zurich