Thanks Seth for your reply...!! I'm trying to analyze a data set of 22691 genes of 73 experiment sets...!! I would like to analyze the significant gene set (positive as well as negatively significant genes) in the dataset above using the same method as cited by Virginia Goss Tusher, Robert Tibshirani, and Gilbert Chu in their paper "Significance analysis of microarrays applied to the ionizing radiation response" 5116-5121, PNAS, April 24, 2001, vol. 98, no. 9. I had already performed samr analysis, but i'm unable to list out the significant genes table using the following command: samr.compute.siggenes.table.obj<-samr.compute.siggenes.table(samr.obj, del,da ta,delta.table,min.foldchange=0) the error message given for this command was: Error in dimnames(res.up) = temp.names : length of 'dimnames' [2] not equal to array extent Hope to hear from you soon. Thanks in advance. Ruma. -----Original Message----- From: Seth Falcon [mailto:sfalcon@fhcrc.org] Sent: Friday, April 27, 2007 8:09 PM To: Ruma Sanyal Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] help for samr "Ruma Sanyal" <rumas at="" cdac.in=""> writes: > Dear all, > > I had been trying to use samr ("One class") for the analysis of a > raw data for my research. the command given by me was : > samr.compute.siggenes.table.obj<-samr.compute.siggenes.table(samr.obj, del,da ta,delta.table,min.foldchange=0) > > I was unable to follow the error message given. Can you please > help me out with the same..??? > the error message give was: > > Error in dimnames(res.up) = temp.names : length of 'dimnames' [2] not > equal to array extent Please read over the posting guide. You will need to provide more detailed information and ideally a reproducible example for us to help you. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org