Hi- I am in the process of analyzing affymetrix data for prostate cancer patients. I have generated expression data with the RMA function and need to do a pairwise comparison. Can someone please help as to what this error means: results <- pairwise.comparison(x.rma, "Phenotype", c("normal", "cancerous"), raw.data) Error in fastT(cbind(a.samples, b.samples), 1:ai, (ai + 1):(ai + bi), : wrong sets of columns Thanks! [[alternative HTML version deleted]]

Hi Lakshmi, First off, you really need to give people more information than this. For instance, what package is pairwise.comparison() in? There are over 350 BioC packages now, so you have to explicitly say what package you are using (people aren't generally going to go to great effort to figure out where this function comes from, just so they can help you). In addition, always give the output of sessionInfo(). On 11/23/2010 2:27 PM, Lakshmi Kastury wrote: > > Hi- > I am in the process of analyzing affymetrix data for prostate cancer patients. I have generated expression data with the RMA function and need to do a pairwise comparison. Can someone please help as to what this error means: > > results<- pairwise.comparison(x.rma, "Phenotype", c("normal", "cancerous"), raw.data) > > Error in fastT(cbind(a.samples, b.samples), 1:ai, (ai + 1):(ai + bi), : > wrong sets of columns This indicates that there is some problem with either the column name you specified or the column values. Or maybe with the code. It's hard to say. I would first ensure that there is a column name "Phenotype" in the pData slot of x.rma, and that there are values "normal","cancerous" in that column. If true, there may be a bug. If there is a bug, the best idea is for you to take things into your own hands and see what is happening. So try library(simpleaffy) debug(get.fold.change.and.t.test) results<- pairwise.comparison(x.rma, "Phenotype", c("normal", "cancerous"), raw.data) then when you enter get.fold.change.and.t.test(), step through and make sure that you are getting reasonable subsets of your data (e.g., a.samples and b.samples look reasonable). Best, Jim > > > Thanks! > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues