[BioC] edgeR for large sample size

[Richard Hu [guest]]

Hi edgeR expert:
   I got a problem in using edgeR for RNA Seq data analysis.   The manual recommends the use of getPriorN to get an appropriate estimate for prior.n used in the algorithm and also warn that prior.n should never be less than 1. Based on the recommended estimation formula prior.n * df = 20 ~ 30 where df = #of samples - #of conditions, it seems that the edgeR package will never work for sample size > 15 for two conditions if 30 is used in the formula, and > 11 if 20 is used in the formula.
   Am I wrong somewhere in understanding the package? I want to make thing sure before I use it because I got more than 100 samples per group in my RNA-seq dataset and the estimate of prior.n << 1. Please be clear that my case is of 100 SAMPLES (or LIBRARIES) NOT 100 GENES or TAGS
   I would appreciate any comments and helps from experts of edgeR
   
   Best 
   Richard Hu
   

 -- output of sessionInfo(): 

R version 2.14.2 (2012-02-29)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] tools_2.14.2

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