Dear Biostars:
The basic design of my RNA-seq experiment is like this:
Tissue Sample Condition
A Sample1 M5
A Sample1 P2
A Sample2 M5
A Sample2 P2
B Sample1 M5
B Sample1 P2
B Sample2 M5
B Sample2 P2
so, I'm following the paired sample design with formula = ~ Tissue+ Tissue:Sample + Tissue:Condition
My question is related to the dispersion estimated by DESeq2. I have estimated the dispersion using all fitType "mean", "local" and "parametric", but none of them seem to work shrinking the gene-wise estimates (please find enclosed the plots).
I know the dispersion fitting depends on several parameters like sample size (Tissue A= 29, Tissue B=37). Now, the question is if this is the best I can get or if there is something else to get a "better" fit.
Thanks!
fitType = Mean > http://imgur.com/uZbsDqr
fitType = local > http://imgur.com/biwXGoL
fitType = Parametric > http://imgur.com/sR0NyzR
