[BioC] edgeR: exactTest different p value in new version 2.4

Gordon K Smyth smyth at wehi.EDU.AU
Fri Nov 18 08:42:41 CET 2011

Dear Sermsawat,

Yes, see the entry for edgeR in:


which says

"A choice of rejection regions is now implemented for exactTest, and the 
default is changed from one based on small probabilities to one based on 
doubling the smaller of the tail probabilities. This gives better results 
than the original conditional test when the dispersion is large 
(especially > 1). A Beta distribution approximation to the tail 
probability is also implemented when the counts are large, allowing 
exactTest() to be much faster and use less memory."

Best wishes

Professor Gordon K Smyth,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
Tel: (03) 9345 2326, Fax (03) 9347 0852,
smyth at wehi.edu.au

On Fri, 18 Nov 2011, Sermsawat Tunlaya-anukit wrote:

> I used edgeR to test differential expression of RNA seq data, but i 
> noticed some different between old version 2.2.5and new version2.4. I 
> compare p value and adjust p value between old version and new one using 
> exactTest() and found that the values are slightly different(logFC and 
> LogConc are the same). Do you change method to calculate p value in the 
> new version?
> Best regards,
> Sermsawat Tunlaya-anukit

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