I was wondering if you could please help me with the following error I keep getting: Error in read.affybatch(filenames = filenames, phenoData = phenoData, : The file C:/Userdata/Desktop/AAA001-U133A.CEL does not look like a CEL file Thanks, Jason

if you make that file available its easier to help. notice that if you are using the new GCOS system you need the latest version of affy (1.4.3) On Sun, 7 Dec 2003, Jason Hipp wrote: > I was wondering if you could please help me with the following error I keep getting: > > Error in read.affybatch(filenames = filenames, phenoData = phenoData, : > The file C:/Userdata/Desktop/AAA001-U133A.CEL does not look like a CEL file > > Thanks, > Jason > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

I don't know if you already got this working but when I last contacted Affy and they told me that if you right click in GCOS (sp?) on the CEL you can export the files and those exports would be in the text-format, since otherwise they are in the binary format. -paul -----Original Message----- From: Jason Hipp [mailto:jhipp@wfubmc.edu] Sent: Sunday, December 07, 2003 12:10 PM To: bioconductor@stat.math.ethz.ch Subject: [BioC] Cel file error I was wondering if you could please help me with the following error I keep getting: Error in read.affybatch(filenames = filenames, phenoData = phenoData, : The file C:/Userdata/Desktop/AAA001-U133A.CEL does not look like a CEL file Thanks, Jason _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

All you need to do is update to the current devel version of affy, which is capable of reading the binary format. Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Paul Grosu <grosu@cgr.harvard.edu> 12/20/03 2:02 AM >>> I don't know if you already got this working but when I last contacted Affy and they told me that if you right click in GCOS (sp?) on the CEL you can export the files and those exports would be in the text-format, since otherwise they are in the binary format. -paul -----Original Message----- From: Jason Hipp [mailto:jhipp@wfubmc.edu] Sent: Sunday, December 07, 2003 12:10 PM To: bioconductor@stat.math.ethz.ch Subject: [BioC] Cel file error I was wondering if you could please help me with the following error I keep getting: Error in read.affybatch(filenames = filenames, phenoData = phenoData, : The file C:/Userdata/Desktop/AAA001-U133A.CEL does not look like a CEL file Thanks, Jason _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

"James MacDonald" <jmacdon@med.umich.edu> writes: > All you need to do is update to the current devel version of affy, which > is capable of reading the binary format. Doesn't the devel version require R-devel, though? Or do we have a version of stable that will read the binary format? best, -tony -- rossini@u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}

Thanks for the clarification (and for others, note that a number of the devel packages now require R-devel (i.e. "1.9"), which was the point of my uncertainity). best, -tony Ben Bolstad <bolstad@stat.berkeley.edu> writes: > Actually the current devel version of affy 1.4.4, which supports the > binary format, runs fine with R-1.8.1. It is likely that this > functionality will be ported to the stable branch at some point. > > Ben > > > On Mon, 2003-12-22 at 05:58, A.J. Rossini wrote: >> "James MacDonald" <jmacdon@med.umich.edu> writes: >> >> > All you need to do is update to the current devel version of affy, which >> > is capable of reading the binary format. >> >> Doesn't the devel version require R-devel, though? Or do we have a >> version of stable that will read the binary format? >> >> best, >> -tony > -- > Ben Bolstad <bolstad@stat.berkeley.edu> > http://www.stat.berkeley.edu/~bolstad > > -- rossini@u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}