[BioC] edgeR: new defaults of estimateTagwiseDisp and exactTest
zhuzhuz at email.unc.edu
Thu Mar 7 01:22:06 CET 2013
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-
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.
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