Affymetrix Command Console CEL files
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Khan, Sohail ▴ 490
@khan-sohail-1137
Last seen 10.3 years ago
Dear member, I am unable to read an Affymetrix Command Console (new Affymetrix Software) generated .cel file by affy function ReadAffy(). I am getting the following error: Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData, : Is M:/Sohail/AGCC_files/JSMK_S428C.CEL really a CEL file? tried reading as text, gzipped text and binary Do these files have to be converted to GCOS format? Or is there an upgrade for the affy package. Thanks. Sohail Khan Scientific Programmer COLD SPRING HARBOR LABORATORY Genome Research Center 500 Sunnyside Boulevard Woodbury, NY 11797 (516)422-4076
affy affy • 1.4k views
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Ben Bolstad ★ 1.2k
@ben-bolstad-1494
Last seen 7.3 years ago
Please give us your sessionInfo(). The affyio package which supplies the parsing routines used by ReadAffy() does have support for this format file (current BioC release version 1.6.1) Ben > Dear member, > > I am unable to read an Affymetrix Command Console (new Affymetrix > Software) generated .cel file by affy function ReadAffy(). > I am getting the following error: > Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData, > : > Is M:/Sohail/AGCC_files/JSMK_S428C.CEL really a CEL file? tried > reading as text, gzipped text and binary > Do these files have to be converted to GCOS format? > Or is there an upgrade for the affy package. > > Thanks. > > > > > Sohail Khan > Scientific Programmer > COLD SPRING HARBOR LABORATORY > Genome Research Center > 500 Sunnyside Boulevard > Woodbury, NY 11797 > (516)422-4076 > > _______________________________________________ > 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 >
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@henrik-bengtsson-4333
Last seen 7 months ago
United States
What's the chip type? For troubleshooting, see if 'affxparser' can read it. /Henrik On 11/1/07, Khan, Sohail <khan at="" cshl.edu=""> wrote: > Dear member, > > I am unable to read an Affymetrix Command Console (new Affymetrix Software) generated .cel file by affy function ReadAffy(). > I am getting the following error: > Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData, : > Is M:/Sohail/AGCC_files/JSMK_S428C.CEL really a CEL file? tried reading as text, gzipped text and binary > Do these files have to be converted to GCOS format? > Or is there an upgrade for the affy package. > > Thanks. > > > > > Sohail Khan > Scientific Programmer > COLD SPRING HARBOR LABORATORY > Genome Research Center > 500 Sunnyside Boulevard > Woodbury, NY 11797 > (516)422-4076 > > _______________________________________________ > 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 >
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@benilton-carvalho-1375
Last seen 4.8 years ago
Brazil/Campinas/UNICAMP
This was addressed recently on affyio and I assume the fix was also applied to the release branch. Try updating affyio. B On Nov 1, 2007, at 11:28 AM, "Khan, Sohail" <khan at="" cshl.edu=""> wrote: > Dear member, > > I am unable to read an Affymetrix Command Console (new Affymetrix > Software) generated .cel file by affy function ReadAffy(). > I am getting the following error: > Error in read.affybatch(filenames = l$filenames, phenoData = l > $phenoData, : > Is M:/Sohail/AGCC_files/JSMK_S428C.CEL really a CEL file? > tried reading as text, gzipped text and binary > Do these files have to be converted to GCOS format? > Or is there an upgrade for the affy package. > > Thanks. > > > > > Sohail Khan > Scientific Programmer > COLD SPRING HARBOR LABORATORY > Genome Research Center > 500 Sunnyside Boulevard > Woodbury, NY 11797 > (516)422-4076 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi, Upgrading R to 2.6.0 and affyio to 1.6.1 solved the problem. Thanks. -Sohail -----Original Message----- From: Benilton Carvalho [mailto:bcarvalh@jhsph.edu] Sent: Thursday, November 01, 2007 11:51 AM To: Khan, Sohail Cc: <bioconductor at="" stat.math.ethz.ch=""> Subject: Re: [BioC] Affymetrix Command Console CEL files This was addressed recently on affyio and I assume the fix was also applied to the release branch. Try updating affyio. B On Nov 1, 2007, at 11:28 AM, "Khan, Sohail" <khan at="" cshl.edu=""> wrote: > Dear member, > > I am unable to read an Affymetrix Command Console (new Affymetrix > Software) generated .cel file by affy function ReadAffy(). > I am getting the following error: > Error in read.affybatch(filenames = l$filenames, phenoData = l > $phenoData, : > Is M:/Sohail/AGCC_files/JSMK_S428C.CEL really a CEL file? > tried reading as text, gzipped text and binary > Do these files have to be converted to GCOS format? > Or is there an upgrade for the affy package. > > Thanks. > > > > > Sohail Khan > Scientific Programmer > COLD SPRING HARBOR LABORATORY > Genome Research Center > 500 Sunnyside Boulevard > Woodbury, NY 11797 > (516)422-4076 > > _______________________________________________ > 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
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