Dear all, I have been looking at using the multtest package for multiple testing correction. specifically on page 5 of the vignette, I have been trying to calculate maxT adjusted p-values for Affymetrix data. However the function will only run a 20 permutations, irrespective of what I set B to. > tmp1 <- eset@exprs > class(tmp1) [1] "matrix" > dim(tmp1) [1] 22690 6 > temp.cats [1] 0 0 0 1 1 1 > resT <- mt.maxT(tmp1, temp.cats) We'll do complete enumerations We're doing 20 complete permutations b=1 b=2 b=3 b=4 b=5 b=6 b=7 b=8 b=9 b=10 b=11 b=12 b=13 b=14 b=15 b=16 b=17 b=18 b=19 b=20 > resT <- mt.maxT(tmp1, temp.cats, B=100000) We'll do complete enumerations We're doing 20 complete permutations b=1 b=2 b=3 b=4 b=5 b=6 b=7 b=8 b=9 b=10 b=11 b=12 b=13 b=14 b=15 b=16 b=17 b=18 b=19 b=20 When I did the example in the vignette, everything worked fine, with the number of permutations equal to B or the default if B was not set. Any ideas? Thanks Claire -- Claire Wilson, PhD Bioinformatics group Paterson Institute for Cancer Research Christies Hospital NHS Trust Wilmslow Road, Withington Manchester M20 4BX tel: +44 (0)161 446 8218 url: http://bioinf.picr.man.ac.uk/ -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}

Dear Claire, As the program is telling you ("We'll do complete enumerations"), it is using complete enumeration, because, it would seem, all Bs you are using are larger than 20. Sensibly, the program will use complete enumeration whenever B > number of permutations under complete enumeration. Hope this helps, Ram?n On Tuesday 19 August 2003 13:43, Claire Wilson wrote: > Dear all, > > I have been looking at using the multtest package for multiple testing > correction. specifically on page 5 of the vignette, I have been trying to > calculate maxT adjusted p-values for Affymetrix data. However the function > will only run a 20 permutations, irrespective of what I set B to. > > > tmp1 <- eset@exprs > > class(tmp1) > > [1] "matrix" > > > dim(tmp1) > > [1] 22690 6 > > > temp.cats > > [1] 0 0 0 1 1 1 > > > resT <- mt.maxT(tmp1, temp.cats) > > We'll do complete enumerations > > We're doing 20 complete permutations > b=1 b=2 b=3 b=4 b=5 b=6 b=7 b=8 b=9 > b=10 > > b=11 b=12 b=13 b=14 b=15 b=16 b=17 b=18 b=19 > b=20 > > > resT <- mt.maxT(tmp1, temp.cats, B=100000) > > We'll do complete enumerations > > We're doing 20 complete permutations > b=1 b=2 b=3 b=4 b=5 b=6 b=7 b=8 b=9 > b=10 > > b=11 b=12 b=13 b=14 b=15 b=16 b=17 b=18 b=19 > b=20 > > > When I did the example in the vignette, everything worked fine, with the > number of permutations equal to B or the default if B was not set. > > Any ideas? > > Thanks > > Claire > > -- > Claire Wilson, PhD > Bioinformatics group > Paterson Institute for Cancer Research > Christies Hospital NHS Trust > Wilmslow Road, > Withington > Manchester > M20 4BX > tel: +44 (0)161 446 8218 > url: http://bioinf.picr.man.ac.uk/ > > -------------------------------------------------------- > > > This email is confidential and intended solely for the use o...{{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://bioinfo.cnio.es/~rdiaz