Hello List, I have a problem performing SAM-analysis. I have 78 array, 47 of them have to be analysed: > dim(exprs(data)[,which(cl==1 | cl==0)]) [1] 54675 47 Vector cl contains the groups for all 78 chips, cl_0 only for those being of interest: > cl [1] 1 1 1 1 NA 1 1 0 0 0 1 1 NA 1 NA NA 0 1 0 NA 0 1 NA 1 1 [26] NA NA 1 NA NA 1 NA 0 NA 1 1 NA NA NA NA NA NA 0 1 NA 0 0 NA 0 0 [51] 0 0 NA NA 1 NA 0 NA NA NA NA NA 1 NA 0 0 0 NA 0 0 NA 0 1 0 0 [76] 0 0 0 > cl_0 [1] 1 1 1 1 1 1 0 0 0 1 1 1 0 1 0 0 1 1 1 1 1 0 1 1 0 1 0 0 0 0 0 0 1 0 1 0 0 0 [39] 0 0 0 1 0 0 0 0 0 SAM works without any problem: sam.out<-sam(exprs(data)[,which(cl==1 | cl==0)],cl_0,rand=123) It is possible to plot the result with plot(sam.out,0.5), but the summary function results in an error message: > sum.sam.out<-summary(sam.out,0.5,ll=FALSE) SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances s0 = 0.0122 (The 0 % quantile of the s values.) Number of permutations: 100 MEAN number of falsely called genes is computed. Delta: 0.5 cutlow: -Inf cutup: 4.25703 p0: 1 Significant Genes: 1 Falsely Called Genes: 0.19 FDR: 0.19 Error in mat.sig[, "d.value"] : incorrect number of dimensions The length of vector cl_0 equals to the columns of exprs(data)[,which(cl==1 | cl==0)]. Do you have any idea? Thanks a lot in advance, Heike -- Dr. Heike Pospisil Center for Bioinformatics, University of Hamburg Bundesstrasse 43, 20146 Hamburg, Germany phone: +49-40-42838-7303 fax: +49-40-42838-7312

On 31 Aug 2005, pospisil at zbh.uni-hamburg.de wrote: > I have a problem performing SAM-analysis. > > I have 78 array, 47 of them have to be analysed: >> dim(exprs(data)[,which(cl==1 | cl==0)]) > [1] 54675 47 > It is possible to plot the result with plot(sam.out,0.5), but the > summary function results in an error message: >> sum.sam.out<-summary(sam.out,0.5,ll=FALSE) > SAM Analysis for the Two-Class Unpaired Case Assuming Unequal > Variances > > s0 = 0.0122 (The 0 % quantile of the s values.) > > Number of permutations: 100 > > MEAN number of falsely called genes is computed. > > Delta: 0.5 > cutlow: -Inf > cutup: 4.25703 > p0: 1 > Significant Genes: 1 > Falsely Called Genes: 0.19 > FDR: 0.19 > > > Error in mat.sig[, "d.value"] : incorrect number of dimensions You might try traceback() just after the error occurs. Folks on the list will also need a bit more info to help you: R version, and versions of the package(s) you are using. The output of session.info() is usually a great start. Best, + seth

Dear Heike, I believe that there is a problem only because you have only one significant gene so that the mat.sig isn't anymore a matrix but a vector. I already have the problem... Hope that helps you Sabrina Sabrina Carpentier Service Bioinformatique Institut Curie - Bat. Trouillet Rossignol (4e ?tage) 26 rue d'Ulm - 75248 Paris Cedex 5 - FRANCE Tel : +33 1 42 34 65 21 ----- Original Message ----- From: "Heike Pospisil" <pospisil@zbh.uni-hamburg.de> To: <bioconductor at="" stat.math.ethz.ch=""> Sent: Wednesday, August 31, 2005 10:10 AM Subject: [BioC] [SAM] Error in mat.sig[,"d.value"] : incorrect number of dimensions > Hello List, > > I have a problem performing SAM-analysis. > > I have 78 array, 47 of them have to be analysed: > > dim(exprs(data)[,which(cl==1 | cl==0)]) > [1] 54675 47 > > > Vector cl contains the groups for all 78 chips, cl_0 only for those being of > interest: > > cl > [1] 1 1 1 1 NA 1 1 0 0 0 1 1 NA 1 NA NA 0 1 0 NA 0 1 NA 1 1 > [26] NA NA 1 NA NA 1 NA 0 NA 1 1 NA NA NA NA NA NA 0 1 NA 0 0 NA 0 0 > [51] 0 0 NA NA 1 NA 0 NA NA NA NA NA 1 NA 0 0 0 NA 0 0 NA 0 1 0 0 > [76] 0 0 0 > > cl_0 > [1] 1 1 1 1 1 1 0 0 0 1 1 1 0 1 0 0 1 1 1 1 1 0 1 1 0 1 0 0 0 0 0 0 1 0 1 0 0 0 > [39] 0 0 0 1 0 0 0 0 0 > > SAM works without any problem: > sam.out<-sam(exprs(data)[,which(cl==1 | cl==0)],cl_0,rand=123) > > It is possible to plot the result with plot(sam.out,0.5), but the summary > function results in an error message: > > sum.sam.out<-summary(sam.out,0.5,ll=FALSE) > SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances > > s0 = 0.0122 (The 0 % quantile of the s values.) > > Number of permutations: 100 > > MEAN number of falsely called genes is computed. > > Delta: 0.5 > cutlow: -Inf > cutup: 4.25703 > p0: 1 > Significant Genes: 1 > Falsely Called Genes: 0.19 > FDR: 0.19 > > > Error in mat.sig[, "d.value"] : incorrect number of dimensions > > The length of vector cl_0 equals to the columns of exprs(data)[,which(cl==1 | > cl==0)]. > Do you have any idea? Thanks a lot in advance, > Heike > -- > Dr. Heike Pospisil > Center for Bioinformatics, University of Hamburg > Bundesstrasse 43, 20146 Hamburg, Germany > phone: +49-40-42838-7303 fax: +49-40-42838-7312 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >