Hi, yes, exactly this is the problem. But this bug has been fixed in siggenes 1.2.17, the Release 1.6 version of Bioconductor. Best, Holger > --- Urspr?ngliche Nachricht --- > Von: "Sabrina Carpentier" <sabrina.carpentier at="" curie.fr=""> > An: "Heike Pospisil" <pospisil at="" zbh.uni-hamburg.de="">, > <bioconductor at="" stat.math.ethz.ch=""> > Betreff: Re: [BioC] [SAM] Error in mat.sig[, "d.value"] : incorrect number > of dimensions > Datum: Wed, 31 Aug 2005 16:39:07 +0200 > > 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 at="" 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 > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > --