Dear Sarah, A problem with your code is that you are trying to read a comma- separated file whereas limma assumes that files are tab-delimited. To read a csv file, you need to specify sep="," in the read.maimages call. If your problem persists, you need to give send the leading lines of your data file, up to the start of the data. Best wishes Gordon > Date: Tue, 1 May 2007 13:55:55 -0500 (CDT) > From: sltucker at artsci.wustl.edu > Subject: Re: [BioC] limma read.maimages for scanarray express .csv > files > To: "Seth Falcon" <sfalcon at="" fhcrc.org=""> > Cc: sltucker at artsci.wustl.edu, bioconductor at stat.math.ethz.ch > > I set my locale to "C", and now have a different error. > >> RG<-read.maimages(files, source="scanarrayexpress", path=path, > columns=list(Rf="Ch1 Median", Rb="Ch1 B Median", Gf="Ch2 Median", Gb= > "Ch2 B Median")) > Error in `[.data.frame`(obj, , columns[[a]]) : > undefined columns selected > > My new sessionInfo() is > >> sessionInfo() > R version 2.4.1 (2006-12-18) > i386-apple-darwin8.8.1 > > locale: > C/C/C/C/C/en_US.UTF-8 > > attached base packages: > [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" > "base" > > other attached packages: > gtools limma > "2.3.0" "2.9.17" > > Thanks! > >> Hi, >> >> [I've put the bioconductor list back in cc, please keep the Q&A >> on-list so that others can benefit too] >> >> sltucker at artsci.wustl.edu writes: >>> Thanks for the help. My sessionInfo() is >>> >>> R version 2.4.1 (2006-12-18) >>> i386-apple-darwin8.8.1 >>> >>> locale: >>> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> It might be worth setting your locale to "C" and seeing if the error >> is the same. >> >> Sys.setlocale(locale="C") >> >> >> + seth >> >> -- >> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research >> Center >> http://bioconductor.org