On Fri, 2007-01-19 at 09:02 +0000, qing Jing wrote: <snip />> Dear All, > > What's wrong?<snip />> I am running R 2.1.1 DBI 0.1-9 RMySQL 0.5-6 Windows XP^^^^^^^^ I'd start with updating your R installation to something less archaic - yours is at least 18 months out of date. Latest version is R 2.4.1.> > Thank you much for your help. > > Qing Jing PhD MDIf you still have problems, first read the posting guide and then email the list, following the instructions in the guide. HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
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.outSAM 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
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 sum.sam.out at row.sig.genes instead of "$" Hope this helps Christoph -------------------------------------------------------------- Credit and Surety PML study: visit our web page www.cs-pml.org -------------------------------------------------------------- Christoph Buser <buser at stat.math.ethz.ch> Seminar fuer Statistik, LEO C13 ETH Zurich 8092 Zurich SWITZERLAND phone: x-41-44-632-4673 fax: 632-1228 http://stat.ethz.ch/~buser/ -------------------------------------------------------------- jing writes: > > > > > Dear all, > > I am running R 2.4.1. > > > library(siggenes); > > library(multtest); > > cl<-rep(c(0,1),c(3,3)); > > sub<-exprs(AffyExpData[,c(1:3,7:9)]); > > gn<-geneNames(AffyRAwData); > > sam.out<-sam(sub,cl,rand=123,gene.names=gn); > > We're doing 20 complete permutations > > > sam.out > SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances > > Delta p0 False Called FDR > 1 0.1 0.929 292.25 293 0.927 > 2 0.4 0.929 43.60 56 0.724 > 3 0.7 0.929 12.25 20 0.569 > 4 1.0 0.929 7.25 14 0.481 > 5 1.3 0.929 2.60 7 0.345 > 6 1.7 0.929 1.30 5 0.242 > 7 2.0 0.929 1.30 5 0.242 > 8 2.3 0.929 0.45 2 0.209 > 9 2.6 0.929 0.45 2 0.209 > 10 2.9 0.929 0.45 2 0.209 > > > sum.sam.out<-summary(sam.out,1,ll=FALSE); > > sum.sam.out$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$row.sig.genes; > NULL > > > Any value of Delta I chosen: 1000,1,0,1 0.00000000001, the outcome is NULL. > > Any help or suggestions that you can provide will be greatly appreciated. > > Qing > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
Or better slot(sum.sam.out, "row.sig.genes") jing writes: > > > > > Dear all, > > I am running R 2.4.1. > > > library(siggenes); > > library(multtest); > > cl<-rep(c(0,1),c(3,3)); > > sub<-exprs(AffyExpData[,c(1:3,7:9)]); > > gn<-geneNames(AffyRAwData); > > sam.out<-sam(sub,cl,rand=123,gene.names=gn); > > We're doing 20 complete permutations > > > sam.out > SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances > > Delta p0 False Called FDR > 1 0.1 0.929 292.25 293 0.927 > 2 0.4 0.929 43.60 56 0.724 > 3 0.7 0.929 12.25 20 0.569 > 4 1.0 0.929 7.25 14 0.481 > 5 1.3 0.929 2.60 7 0.345 > 6 1.7 0.929 1.30 5 0.242 > 7 2.0 0.929 1.30 5 0.242 > 8 2.3 0.929 0.45 2 0.209 > 9 2.6 0.929 0.45 2 0.209 > 10 2.9 0.929 0.45 2 0.209 > > > sum.sam.out<-summary(sam.out,1,ll=FALSE); > > sum.sam.out$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 at 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.