I have not installed the package "siggenes", but from the manual on"
http://www.ugrad.stat.ubc.ca/R/library/siggenes/ I assume it is programmed as an S4 class since they use [EMAIL PROTECTED] instead of "$" Hope this helps Christoph -------------------------------------------------------------- Credit and Surety PML study: visit our web page www.cs-pml.org -------------------------------------------------------------- Christoph Buser <[EMAIL PROTECTED]> Seminar fuer Statistik, LEO C13 ETH Zurich 8092 Zurich SWITZERLAND phone: x-41-44-632-4673 fax: 632-1228 http://stat.ethz.ch/~buser/ -------------------------------------------------------------- jing writes: > > > > > Dear all, > > I am running R 2.4.1. > > > library(siggenes); > > library(multtest); > > cl<-rep(c(0,1),c(3,3)); > > sub<-exprs(AffyExpData[,c(1:3,7:9)]); > > gn<-geneNames(AffyRAwData); > > sam.out<-sam(sub,cl,rand=123,gene.names=gn); > > We're doing 20 complete permutations > > > sam.out > SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances > > Delta p0 False Called FDR > 1 0.1 0.929 292.25 293 0.927 > 2 0.4 0.929 43.60 56 0.724 > 3 0.7 0.929 12.25 20 0.569 > 4 1.0 0.929 7.25 14 0.481 > 5 1.3 0.929 2.60 7 0.345 > 6 1.7 0.929 1.30 5 0.242 > 7 2.0 0.929 1.30 5 0.242 > 8 2.3 0.929 0.45 2 0.209 > 9 2.6 0.929 0.45 2 0.209 > 10 2.9 0.929 0.45 2 0.209 > > > sum.sam.out<-summary(sam.out,1,ll=FALSE); > > sum.sam.out$row.sig.genes; > NULL > > sum.sam.out<-summary(sam.out,0.1,ll=FALSE); > > sum.sam.out$row.sig.genes; > NULL > > sum.sam.out<-summary(sam.out,0.00000000001,ll=FALSE); > > sum.sam.out$row.sig.genes; > NULL > > sum.sam.out<-summary(sam.out,1000,ll=FALSE); > > sum.sam.out$row.sig.genes; > NULL > > > Any value of Delta I chosen: 1000,1,0,1 0.00000000001, the outcome is NULL. > > Any help or suggestions that you can provide will be greatly appreciated. > > Qing > > ______________________________________________ > R-help@stat.math.ethz.ch 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. ______________________________________________ R-help@stat.math.ethz.ch 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.
