Hi Stephen, I have started using the package 'multtest', and I have it working, but I have a few questions which probably show I don't really know how the package is working! 1. The following commands will provide a count of probe sets that fall into each defined category and create a vector of probe sets that meet a specified criteria, but I don't understand what the $r or $which are doing on the end of these commands, I realize they are necessary, but... >mt.reject(cbind(RawpvT,maxT),seq(0,1,0.1))$r & which<-mt.reject(cbind(RawpvT,maxT),0.01)$which[,2]. 2. Is there an easy way to get a list of the probe sets and their associated p-values (raw and adjusted) that meet a specified criteria in a single data frame/matrix? Thanks, Rich Rich Roth, PhD Senior Scientist, Bioinformatics Molecular Medicine Neurocrine Biosciences 858-617-7204 -------------- next part -------------- "MMS <neurocrine.com>" made the following annotations on 03/21/2006 11:59:21 AM ---------------------------------------------------------------------- -------- This email may contain confidential and privileged material ...{{dropped}}

I don't much use multtest itself preferring the built in methods that go with limma (e.g. toptable). I think however you would be better using the 'mt.rawp2adjp' function. e.g ## using Benjamini-Hochberg (or something like that) > mt.rawp2adjp(p, "BH")->rej > rej$adjp[1:3,] rawp BH [1,] 3.245434e-17 1.477904e-12 [2,] 5.406144e-17 1.477904e-12 [3,] 8.744990e-15 1.593774e-10 >cutoff<-.05 ## i.e which in the the BH column do you want > wh<-which (rej$adjp[,2]< cutoff) ## the adjp list is sorted the index to genes is in rej$index > ind <- rej$index[wh] ## you want something like cbind(geneNames(myEset)[ind], rej$adjp[wh,])-> output ## or use geneNames(myEset)[ind] to query the annotation packages for symbols, refseqs etc. Cheers Stephen Henderson Wolfson Inst. for Biomedical Research Cruciform Bldg., Gower Street University College London United Kingdom, WC1E 6BT +44 (0)207 679 6827 -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Roth, Richard Sent: 21 March 2006 19:59 To: bioconductor at stat.math.ethz.ch Subject: [BioC] Multtest Hi Stephen, I have started using the package 'multtest', and I have it working, but I have a few questions which probably show I don't really know how the package is working! 1. The following commands will provide a count of probe sets that fall into each defined category and create a vector of probe sets that meet a specified criteria, but I don't understand what the $r or $which are doing on the end of these commands, I realize they are necessary, but... >mt.reject(cbind(RawpvT,maxT),seq(0,1,0.1))$r & which<-mt.reject(cbind(RawpvT,maxT),0.01)$which[,2]. 2. Is there an easy way to get a list of the probe sets and their associated p-values (raw and adjusted) that meet a specified criteria in a single data frame/matrix? Thanks, Rich Rich Roth, PhD Senior Scientist, Bioinformatics Molecular Medicine Neurocrine Biosciences 858-617-7204 ********************************************************************** This email and any files transmitted with it are confidentia...{{dropped}}