Søren Faurby wrote: > In an effort to select the most appropriate number of clusters in a > mixture analysis I am comparing the expected and actual membership of > individuals in various clusters using the Fisher?s exact test. I aim > for the model with the lowest possible p-value, but I frequently get > p-values below 2.2e-16 and therefore does not get exact p-values with > standard Fisher?s exact tests in R. > > Does anybody know if there is a version of Fisher?s exact test in > any package which can handle lower probabilities, or have other > suggestions as to how I can compare the probabilities? > > I am for instance comparing the following two: > > dat2<-matrix(c(29,0,29,0,12,0,18,0,0,29,0,16,0,19), nrow=2) > fisher.test(dat2, workspace=30000000) > > dat3<-matrix(c(29,0,0,29,0,0,12,0,0,17,0,1,0,29,0,0,15,1,0,0,19), > nrow=3) > fisher.test(dat3, workspace=30000000) > > Which both result in p-value < 2.2e-16 > > Kind regards, Søren
The direct answer is that it is primarily an issue of printing conventions: > fisher.test(dat2, workspace=30000000)$p.value [1] 5.384278e-44 > fisher.test(dat3, workspace=30000000)$p.value [1] 5.883133e-58 However, I'm not sure (a) what is the influence of underflow in the calculation of such tiny p-values, or (b) whether the p-value is a sensible metric for comparing clustering models at all. -- O__ ---- Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
