You can also type news(package="edgeR") at the R prompt to see the same information. Best wishes Gordon On Fri, 18 Nov 2011, Gordon K Smyth wrote: > Dear Sermsawat, > > Yes, see the entry for edgeR in: > > http://www.bioconductor.org/news/bioc_2_9_release/ > > 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 > Gordon > > --------------------------------------------- > 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 > http://www.wehi.edu.au > http://www.statsci.org/smyth > > 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 > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}