Hi, is it possible to read a file for the sam calculation with the gene names in the same table. The first column was with gene names, the next four were with experiments and the next 14 were the controls. I've tried this way: >last.data <- read.delim2("AE0625419_genenames.txt") >last.out <- sam(last.data, AE0627999.cl, B=20, gene.names=matrix_all_names[,2]) But i get this message: Fehler in adjust.for.mt(data, cl, var.equal = var.equal) : The length of cl must be equal to the number of columns of data. Zus?tzlich: Warning messages: 1: NAs durch Umwandlung erzeugt 2: There are 22811 genes with at least one missing expression value. The NAs are replaced by the gene-wise mean. 3: 22791 of the 22811 genes with at least one NA have no and 20 have one non-missing expression value. All these 22811 genes are removed, and their d-values are set to NA. Is there a way of telling sam to ignore the first columns for the cl- vector? THX, Assa -- Assa Yeroslaviz L?tzenerstr. 15 51373 Leverkusen

On Nov 2, 2005, at 7:51 AM, Assa Yeroslaviz wrote: > Hi, > > is it possible to read a file for the sam calculation with the gene > names in the > same table. > The first column was with gene names, the next four were with > experiments and > the next 14 were the controls. > I've tried this way: > >> last.data <- read.delim2("AE0625419_genenames.txt") >> last.out <- sam(last.data, AE0627999.cl, B=20, >> gene.names=matrix_all_names[,2]) > > But i get this message: > Fehler in adjust.for.mt(data, cl, var.equal = var.equal) : > The length of cl must be equal to the number of columns of > data. > Zus?tzlich: Warning messages: > 1: NAs durch Umwandlung erzeugt > 2: There are 22811 genes with at least one missing expression value. > The NAs are replaced by the gene-wise mean. > 3: 22791 of the 22811 genes with at least one NA have no and 20 > have one > non-missing expression value. > All these 22811 genes are removed, and their d-values are set to NA. > > Is there a way of telling sam to ignore the first columns for the > cl-vector? If I understand you correctly, cl is a matrix (or a data.frame). if that is true, just selct the appropriate column by AE0627999$columnName or AE0627999[,1] (for the first column) Kasper > THX, > > Assa > > -- > Assa Yeroslaviz > L?tzenerstr. 15 > 51373 Leverkusen > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor