Hi Mark, Yes you are right I was using an old version of the vignette ... sorry about that. As for the design decision I have two suggestions: 1) A new function that simplifies exactTestNB (or modify exactTestNB itself) so that you only have to provide an EBList-class object and the groups (if more than two) and it returns a vector of results from the exact test 2) If there is two groups provide an $exact element from deDGE, but if not don't. Thanks Dan Mark Robinson wrote: > Hi Daniel. > > Thanks for the note. Indeed, there was a change in the package there as > to where the exact p-values get calculated. I have mixed feeling on > this, but the decision to move this to topTags() was based on the fact > that we now support multiple groups yet the exact test is only realistic > for 2-group comparisons. In topTags(), you must specify the pairwise > difference of interest. I would welcome your feedback on this design > decision as like I said, I have mixed feelings of how this should be > done. The alternative is to precompute all the pairwise exact tests in > deDGE() and maintain the $exact element. > > As to the vignette example, I suspect you are using an older vignette. > The vignette for 1.2.x illustrates the same example with updated code. > > Hope that helps. > Mark > > > On 12-Aug-09, at 8:57 PM, Daniel Brewer wrote: > >> It use to be that when you run deDGE from the edgeR library that it >> calculated the Fisher exact p-values and put it in a slot "exact". This >> no longer seems to be the case, with the p-values only being calculated >> when topTags() is called. This means that the plot example in the >> vignette no longer works i.e. >> >>> adj.p <- p.adjust(ms$exact, "fdr") >>> k <- (adj.p < 0.05) >>> plotMA(ms, col = c("black", "blue")[k + 1]) >> >> Have I missed something? How do you get round this? >> >> Thanks >> >> Dan >> -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:2}}