[BioC] edgeR: new defaults of estimateTagwiseDisp and exactTest

[Zhuzhu Zhang]

Dear All,

I'm running edgeR 3.0.8 and notice that the results are considerably 
different than those from older versions. I realized that it was likely 
due to the different prior.df I used in Function estimateTagwiseDisp, 
thanks to an earlier discussion on the list-
https://stat.ethz.ch/pipermail/bioconductor/2012-December/049644.html

I have a few more questions:

1. How to choose a proper prior.df (or prior.n)?

2. How is the new default method of exactText different from the old 
default (rejection.region = "smallp")? How does it improve the performance?

3. In general, what parameters should I tune for different datasets, 
when using function estimateTagwiseDisp and exactTest? I used the 
defaults but realized that they may not be most appropriate.

Thank you for your time and attention. Any suggestions and comments 
would be extremely helpful and appreciated.

Thanks,
Zhuzhu