I am a new user of the RankProd package and am having difficulty getting it to work with my data, whereas I have no problem with the golub data used in the vignette. The RankProd functions run fine and do not produce errors with my data, but I get no significant genes, whereas the same data with Limma and SAM produce over a thousand sig. genes at FDR<0.1. I can't help but think I am making a silly mistake in setting up the cl or origen vectors for RankProd or perhaps in something else. Below is my sessionInfo() and script for both Limma and RankProd. Any help would be appreciated. Thanks, Mark sessionInfo() R version 2.4.0 (2006-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "splines" "stats" "graphics" "grDevices" "datasets" "utils" "methods" "tools" "base" other attached packages: rgu34acdf svMisc multtest affycoretools biomaRt RCurl XML GOstats "1.14.0" "0.9-5" "1.12.0" "1.6.0" "1.8.0" "0.7-0" "0.99-93" "2.0.3" Category genefilter survival KEGG RBGL annotate GO graph "2.0.3" "1.12.0" "2.29" "1.14.1" "1.10.0" "1.12.0" "1.14.1" "1.12.0" RankProd RWinEdt limma affy affyio Biobase "2.6.0" "1.7-5" "2.9.1" "1.12.1" "1.2.0" "1.12.2" ##################################### #The Limma method require(limma) factor.mat<-factor(pData(affy.object.preprocessed.BB01$eSet)$Treatment ) #affy.object.preprocessed.BB01$eSet is the # expressionSet created with justRMA treatments <- factor(factor.mat) #Treatment has two levels, P and NP design <- model.matrix(~ -1+treatments) colNames <- unique(factor.mat); o<-order(colNames); colNames<-colNames[o]; colnames(design)<-colNames fit <- lmFit(exprs(affy.object.preprocessed.BB01$eSet),des=design) ###################################################################### ## #Make contrast matrix contrast <-makeContrasts( (P - NP), levels=design) ###################################################################### ##### fit2 <- contrasts.fit(fit,contrast) fit2<-eBayes(fit2) rslt <- decideTests(fit2, method="separate", adjust.method="BH",p.value=0.1) topTable(fit2,coef=1,number=10,genelist=fit$genes,adjust.method="BH",s ort.by="B",resort.by=NULL) ###################################################################### ### #The RankProd method RP.out<-RPadvance(data=exprs(affy.object.preprocessed.BB01$eSet), cl=c(as.numeric(unclass(factor(pData(affy.object.preprocessed.BB01 $eSet)$Treatment))) - 1), origin=rep(1, ncol(exprs(affy.object.preprocessed.BB01$eSet))), num.perm=100, logged=TRUE, na.rm=FALSE, gene.names=NULL, plot=TRUE, rand=NULL) plotRP(RP.out, cutoff=0.1) topGene(RP.out,cutoff = 0.1, logged = TRUE, logbase = 2, gene.names=affy.object.preprocessed.BB01$annotations[,4]) Mark W. Kimpel MD ? Official Business Address: ? Department of Psychiatry Indiana University School of Medicine PR M116 Institute of Psychiatric Research 791 Union Drive Indianapolis, IN 46202 ? Preferred Mailing Address: ? 15032 Hunter Court Westfield, IN? 46074 ? (317) 490-5129 Work, & Mobile ? (317) 663-0513 Home (no voice mail please) 1-(317)-536-2730 FAX