while i m trying to use the new samr it happens that i don t really know how many parameters to enter, here is an example > sam_NMM.output <- + sam.wilc(samOvary_NMM,samOvary_NMM.cl,delta=NULL,n.delta=10,p0=NA, + lambda=seq(0,0.95,0.05),ncs.value="max",ncs.weights=NULL, + gene.names=dimnames(samOvary_NMM)[[1]],q.version=1,R.fold=1, + R.unlog=TRUE,na.replace=TRUE,na.method="median",approx50=FALSE, + check.ties=TRUE,rand=123) Error in substring(gene.neames, 1, 50) : Object "gene.neames" not found In addition: Warning message: There are 1 genes with ties. The ranks of these ties are randomly assigned. but in any conbination of parameters that i use i always have the same output:>Error in substring(gene.neames, 1, 50) : Object "gene.neames" not found In addition: Warning message: There are 1 genes with ties. The ranks of these ties are randomly assigned.< thanks -------------------------------------------------- D.Enrique ESCOBAR ESPINOZA B.Sc.) http://adn.bioinfo.uqam.ca/~escd07097301/ ICQ#: 201778618 ------------------------------------------------- 1487, Boul. St-Joseph Est Apt4 Tel: (514) 523-8398 Montreal QC Canada H2J 1M6

Hi, oh, this is a bug in sam.wilc. It should be substring(gene.names,1,50) and not substring(gene.neames,1,50). I actually thought that I have removed this bug. I will immediately fix this bug. But you can still do your analysis with the Wilcoxon rank sums by using > sam(data,cl,method="wilc.stat",...) instead of > sam.wilc(data,cl,...) This will work and give you the same results. Another solution would be to set gene.names=NULL in sam.wilc. Best, Holger > --- Urspr?ngliche Nachricht --- > Von: "D.Enrique ESCOBAR ESPINOZA" <escobarebio at="" yahoo.com=""> > An: bioconductor at stat.math.ethz.ch > Betreff: [BioC] sam > Datum: Tue, 21 Jun 2005 07:59:20 -0700 (PDT) > > while i m trying to use > the new samr > it happens that i don t really know how many parameters to enter, > here is an example > > sam_NMM.output <- > + sam.wilc(samOvary_NMM,samOvary_NMM.cl,delta=NULL,n.delta=10,p0=NA, > + lambda=seq(0,0.95,0.05),ncs.value="max",ncs.weights=NULL, > + gene.names=dimnames(samOvary_NMM)[[1]],q.version=1,R.fold=1, > + R.unlog=TRUE,na.replace=TRUE,na.method="median",approx50=FALSE, > + check.ties=TRUE,rand=123) > Error in substring(gene.neames, 1, 50) : Object "gene.neames" not > found > In addition: Warning message: > There are 1 genes with ties. The ranks of these ties are randomly > assigned. > > but in any conbination of parameters that i use i always have the > same > output:>Error in substring(gene.neames, 1, 50) : Object "gene.neames" > not found > In addition: Warning message: > There are 1 genes with ties. The ranks of these ties are randomly > assigned.< > thanks > > -------------------------------------------------- > D.Enrique ESCOBAR ESPINOZA B.Sc.) > http://adn.bioinfo.uqam.ca/~escd07097301/ > ICQ#: 201778618 > ------------------------------------------------- > 1487, Boul. St-Joseph Est Apt4 > Tel: (514) 523-8398 > Montreal QC Canada > H2J 1M6 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > --