i am having trouble opening my .CEL files in affylmGUI. i get an error message: Failed to open file: "Foo.CEL" my best guess is that my .CEL files are all moe430a_2 and this does not have an annotation package. or does this file need to be binary?? afflmGUI 1.1.0 limma 1.6.6 R 1.9.0 BioC 1.4 -isaac --

Hi, I don't know much about the differences in the way the affy package handles different CEL file formats (binary or other), but I can at least mention that affylmGUI expects you to set your working directory to the directory containing the CEL files, and then the CEL files listed in the Targets file don't need to have any absolute file paths, just a file name (expected to be in the current working directory). I haven't tested much with Targets files that have absolute file paths. Of course if you want to help us to isolate the error, you could try reading the CEL file at the command-line, with : library(affy) rawAffyData <- ReadAffy(filenames="foo.CEL") Then you can tell whether the error is more related to affylmGUI or to affy. Hope this helps, James On Tue, 22 Jun 2004, Isaac Mehl wrote: > i am having trouble opening my .CEL files in affylmGUI. i get an error > message: > Failed to open file: "Foo.CEL" > my best guess is that my .CEL files are all moe430a_2 and this does not > have an annotation package. or does this file need to be binary?? > afflmGUI 1.1.0 > limma 1.6.6 > R 1.9.0 > BioC 1.4 > > -isaac > -- > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > -- ---------------------------------------------------------------------- ---- James Wettenhall Tel: (+61 3) 9345 2629 Division of Genetics and Bioinformatics Fax: (+61 3) 9347 0852 The Walter & Eliza Hall Institute E-mail: wettenhall@wehi.edu.au of Medical Research, Mobile: (+61 / 0 ) 438 527 921 1G Royal Parade, Parkville, Vic 3050, Australia http://www.wehi.edu.au