Hi James, Your problem lies in the read.affybatch function (ReadAffy is a wrapper of this). if you look inside the guts of read.affybatch you'll see where your error is coming from: if (dim(pdata)[1] != n) { warning("Incompatible phenoData object. Created a new one.\n") samplenames <- sub("^/?([^/]*/)*", "", filenames, extended = TRUE) pdata <- data.frame(sample = 1:n, row.names = samplenames) phenoData <- new("AnnotatedDataFrame", data = pdata, varMetadata = data.frame(labelDescription = "arbitrary numbering", row.names = "sample")) } Looks to me like the the phenoData AnnotatedDataFrame is being triggered, because on isn't supplied it tries to make one. This is then resulting in substitution being attempted on the list of filenames as it tries to get something to use as the samplenames. However the error is that it is not able to use the extended=TRUE. Have a look at the help file for sub function to see how to setup Perl Compatible Regular Expression on your system (PCRE). The regular expressions used are those specified by POSIX 1003.2, either extended or basic, depending on the value of the extended argument, unless perl = TRUE when they are those of PCRE, http://www.pcre.org/. (The exact set of patterns supported may depend on the version of PCRE installed on the system in use if *R* was configured to use the system PCRE.) That should hopefully take care of the problem. Rdgs, Amos Folarin ---------- Forwarded message ---------- From: "James W. MacDonald" <jmacdon@med.umich.edu> To: mandova <mandova1005@yahoo.cn> Date: Wed, 04 Aug 2010 15:33:08 -0400 Subject: Re: [BioC] [R] error with ReadAffy() This question is more appropriate for the bioconductor list < bioconductor@stat.math.ethz.ch>. I have cc'ed there. Any time you ask a question, you need to give the output of sessionInfo(), so please give us that output. Best, Jim On 8/4/10 9:08 AM, mandova wrote: > Hi!I'm doing a little data importing from .cel files, > > setwd("/home/mandova/celfiles") >> mydata<-ReadAffy() >> > Error in sub("^/?([^/]*/)*", "", filenames, extended = TRUE) : > unused argument(s) (extended = TRUE) > > > Then I tried > >> filenames<-paste("GSM",c(seq(138597,138617,1)),".cel",sep="") >> filenames<-as.character(filenames) >> filenames >> > > [1] "GSM138597.cel" "GSM138598.cel" "GSM138599.cel" "GSM138600.cel" > [5] "GSM138601.cel" "GSM138602.cel" "GSM138603.cel" "GSM138604.cel" > [9] "GSM138605.cel" "GSM138606.cel" "GSM138607.cel" "GSM138608.cel" > [13] "GSM138609.cel" "GSM138610.cel" "GSM138611.cel" "GSM138612.cel" > [17] "GSM138613.cel" "GSM138614.cel" "GSM138615.cel" "GSM138616.cel" > [21] "GSM138617.cel" > > mydata<-ReadAffy(compress=FALSE,filenames=filenames) >> > Error in sub("^/?([^/]*/)*", "", filenames, extended = TRUE) : > unused argument(s) (extended = TRUE) > > Same error! Could you please help me understand the error message? Thx!!! > > -- 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 [[alternative HTML version deleted]]