affxparser fails to convert AGCC format cel file
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@steiner-guido-2421
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Ben Bolstad ★ 1.2k
@ben-bolstad-1494
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I can't speak for affxparser (which I am sure has support for these files in some way), but the latest version of affyio (the one in the recent BioC 2.1 release) should handle AGCC format cel files (and gzipped versions of the same, keeping with historical support patterns). What does this mean? It means if you use ReadAffy() to create your affybatch it should be automatically handled. Best, Ben > Hi, > > I just tried affxparser on an example CEL file from the new Affymetrix > > Command Console software. > > > >> library(affxparser) > >> convertCel("agcc.cel","gcos.cel") > > Error in sprintf("DatHeader=%s\n", datHeader) : zero-length argument > > > >> createCel("test.cel",header=readCelHeader("agcc.cel")) > > Error in sprintf("DatHeader=%s\n", datHeader) : zero-length argument > > > > So the error seems to happen at the createCell stage already. > > Reading the cel file with readCel does work! > > I have R 2.6.0/BioC 2.1 and affxparser version 1.10.0. > > Chip type is RAT_230 (I can provide the cel file if someone is > > interested). > > > > Any ideas how to solve this? (As an alternative - it would be fully > > sufficient for me to use readCel if there was a method to get the > > output into an AffyBatch object.) > > > > Regards, > > Guido > > > > > > -- > Guido Steiner, PhD > F. Hoffmann-La Roche AG > PRBI-M Scientific Methods and Algorithms > Building 65/318B > CH-4070 Basel > Tel. +41 61 688 3329 > > Confidentiality Note: This message is intended only for ...{{dropped:12}} > > _______________________________________________ > 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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Ben, ReadAffy() is (not surprisingly, maybe) the first thing I tried to import the file. This is what happened: *** caught segfault *** address 0x1ffffffffffffff8, cause 'memory not mapped' Traceback: 1: .Call("read_abatch", filenames, rm.mask, rm.outliers, rm.extra, ref.cdfName, dim.intensity, verbose, PACKAGE = "affyio") 2: read.affybatch(filenames = l$filenames, phenoData = l$phenoData, description = l$description, notes = notes, compress = compress, rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, verbose = verbose, sd = sd, cdfname = cdfname) 3: ReadAffy("17F_Liver_TXST20060258.CEL") -----Original Message----- From: bmb@bmbolstad.com [mailto:bmb@bmbolstad.com] Sent: Wednesday, October 10, 2007 3:46 PM To: Steiner, Guido {PRBI~Basel} Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] affxparser fails to convert AGCC format cel file I can't speak for affxparser (which I am sure has support for these files in some way), but the latest version of affyio (the one in the recent BioC 2.1 release) should handle AGCC format cel files (and gzipped versions of the same, keeping with historical support patterns). What does this mean? It means if you use ReadAffy() to create your affybatch it should be automatically handled. Best, Ben > Hi, > > I just tried affxparser on an example CEL file from the new Affymetrix > > Command Console software. > > > >> library(affxparser) > >> convertCel("agcc.cel","gcos.cel") > > Error in sprintf("DatHeader=%s\n", datHeader) : zero-length argument > > > >> createCel("test.cel",header=readCelHeader("agcc.cel")) > > Error in sprintf("DatHeader=%s\n", datHeader) : zero-length argument > > > > So the error seems to happen at the createCell stage already. > > Reading the cel file with readCel does work! > > I have R 2.6.0/BioC 2.1 and affxparser version 1.10.0. > > Chip type is RAT_230 (I can provide the cel file if someone is > > interested). > > > > Any ideas how to solve this? (As an alternative - it would be fully > > sufficient for me to use readCel if there was a method to get the > > output into an AffyBatch object.) > > > > Regards, > > Guido > > > > > > -- > Guido Steiner, PhD > F. Hoffmann-La Roche AG > PRBI-M Scientific Methods and Algorithms > Building 65/318B > CH-4070 Basel > Tel. +41 61 688 3329 > > Confidentiality Note: This message is intended only for ...{{dropped:12}} > > _______________________________________________ > 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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Could you give us your sessionInfo()? One guess might be that your file is in someway corrupted? I would be happy to take your cel file and have a look at it. Best, Ben > > Ben, > ReadAffy() is (not surprisingly, maybe) the first thing I tried > to import the file. This is what happened: > > *** caught segfault *** > address 0x1ffffffffffffff8, cause 'memory not mapped' > > Traceback: > 1: .Call("read_abatch", filenames, rm.mask, rm.outliers, rm.extra, > ref.cdfName, dim.intensity, verbose, PACKAGE = "affyio") > 2: read.affybatch(filenames = l$filenames, phenoData = l$phenoData, > description = l$description, notes = notes, compress = compress, > rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, > verbose = verbose, sd = sd, cdfname = cdfname) > 3: ReadAffy("17F_Liver_TXST20060258.CEL") > > > > > -----Original Message----- > From: bmb at bmbolstad.com [mailto:bmb at bmbolstad.com] > Sent: Wednesday, October 10, 2007 3:46 PM > To: Steiner, Guido {PRBI~Basel} > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] affxparser fails to convert AGCC format cel file > > I can't speak for affxparser (which I am sure has support for these > files > in some way), but the latest version of affyio (the one in the recent > BioC > 2.1 release) should handle AGCC format cel files (and gzipped versions > of > the same, keeping with historical support patterns). What does this > mean? > It means if you use ReadAffy() to create your affybatch it should be > automatically handled. > > Best, > > Ben > > > >> Hi, >> >> I just tried affxparser on an example CEL file from the new Affymetrix >> >> Command Console software. >> >> >> >>> library(affxparser) >> >>> convertCel("agcc.cel","gcos.cel") >> >> Error in sprintf("DatHeader=%s\n", datHeader) : zero-length argument >> >> >> >>> createCel("test.cel",header=readCelHeader("agcc.cel")) >> >> Error in sprintf("DatHeader=%s\n", datHeader) : zero-length argument >> >> >> >> So the error seems to happen at the createCell stage already. >> >> Reading the cel file with readCel does work! >> >> I have R 2.6.0/BioC 2.1 and affxparser version 1.10.0. >> >> Chip type is RAT_230 (I can provide the cel file if someone is >> >> interested). >> >> >> >> Any ideas how to solve this? (As an alternative - it would be fully >> >> sufficient for me to use readCel if there was a method to get the >> >> output into an AffyBatch object.) >> >> >> >> Regards, >> >> Guido >> >> >> >> >> >> -- >> Guido Steiner, PhD >> F. Hoffmann-La Roche AG >> PRBI-M Scientific Methods and Algorithms >> Building 65/318B >> CH-4070 Basel >> Tel. +41 61 688 3329 >> >> Confidentiality Note: This message is intended only for > ...{{dropped:12}} >> >> _______________________________________________ >> 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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Ben, that's a very kind offer which I am delighted to accept. Cel data will fly directly to you, and here's the sessionInfo for the others as well. Best, Guido R version 2.6.0 (2007-10-03) ia64-unknown-linux-gnu locale: C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.0 [4] Biobase_1.16.0 loaded via a namespace (and not attached): [1] rcompgen_0.1-15 -----Original Message----- From: bmb@bmbolstad.com [mailto:bmb@bmbolstad.com] Sent: Wednesday, October 10, 2007 5:24 PM To: Steiner, Guido {PRBI~Basel} Cc: bmb at bmbolstad.com; bioconductor at stat.math.ethz.ch Subject: RE: [BioC] affxparser fails to convert AGCC format cel file Could you give us your sessionInfo()? One guess might be that your file is in someway corrupted? I would be happy to take your cel file and have a look at it. Best, Ben > > Ben, > ReadAffy() is (not surprisingly, maybe) the first thing I tried > to import the file. This is what happened: > > *** caught segfault *** > address 0x1ffffffffffffff8, cause 'memory not mapped' > > Traceback: > 1: .Call("read_abatch", filenames, rm.mask, rm.outliers, rm.extra, > ref.cdfName, dim.intensity, verbose, PACKAGE = "affyio") > 2: read.affybatch(filenames = l$filenames, phenoData = l$phenoData, > description = l$description, notes = notes, compress = compress, > rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, > verbose = verbose, sd = sd, cdfname = cdfname) > 3: ReadAffy("17F_Liver_TXST20060258.CEL") > > > > > -----Original Message----- > From: bmb at bmbolstad.com [mailto:bmb at bmbolstad.com] > Sent: Wednesday, October 10, 2007 3:46 PM > To: Steiner, Guido {PRBI~Basel} > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] affxparser fails to convert AGCC format cel file > > I can't speak for affxparser (which I am sure has support for these > files > in some way), but the latest version of affyio (the one in the recent > BioC > 2.1 release) should handle AGCC format cel files (and gzipped versions > of > the same, keeping with historical support patterns). What does this > mean? > It means if you use ReadAffy() to create your affybatch it should be > automatically handled. > > Best, > > Ben > > > >> Hi, >> >> I just tried affxparser on an example CEL file from the new Affymetrix >> >> Command Console software. >> >> >> >>> library(affxparser) >> >>> convertCel("agcc.cel","gcos.cel") >> >> Error in sprintf("DatHeader=%s\n", datHeader) : zero-length argument >> >> >> >>> createCel("test.cel",header=readCelHeader("agcc.cel")) >> >> Error in sprintf("DatHeader=%s\n", datHeader) : zero-length argument >> >> >> >> So the error seems to happen at the createCell stage already. >> >> Reading the cel file with readCel does work! >> >> I have R 2.6.0/BioC 2.1 and affxparser version 1.10.0. >> >> Chip type is RAT_230 (I can provide the cel file if someone is >> >> interested). >> >> >> >> Any ideas how to solve this? (As an alternative - it would be fully >> >> sufficient for me to use readCel if there was a method to get the >> >> output into an AffyBatch object.) >> >> >> >> Regards, >> >> Guido >> >> >> >> >> >> -- >> Guido Steiner, PhD >> F. Hoffmann-La Roche AG >> PRBI-M Scientific Methods and Algorithms >> Building 65/318B >> CH-4070 Basel >> Tel. +41 61 688 3329 >> >> Confidentiality Note: This message is intended only for > ...{{dropped:12}} >> >> _______________________________________________ >> 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
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Hi Guido, regarding affxparser: When writing a v4 CEL header, affxparser need the DAT header, which is not readily available in AGCC CEL files so affxparser will try to generate a valid one from what is available. It seems like it fails in this case. I cannot say more until I see the CEL file. Please let me (here or offline) know how I can download this CEL file (I cannot receive attachments > 19MB). /Henrik On 10/10/07, Steiner, Guido <guido.steiner at="" roche.com=""> wrote: > Hi, > > I just tried affxparser on an example CEL file from the new Affymetrix > > Command Console software. > > > > > library(affxparser) > > > convertCel("agcc.cel","gcos.cel") > > Error in sprintf("DatHeader=%s\n", datHeader) : zero-length argument > > > > > createCel("test.cel",header=readCelHeader("agcc.cel")) > > Error in sprintf("DatHeader=%s\n", datHeader) : zero-length argument > > > > So the error seems to happen at the createCell stage already. > > Reading the cel file with readCel does work! > > I have R 2.6.0/BioC 2.1 and affxparser version 1.10.0. > > Chip type is RAT_230 (I can provide the cel file if someone is > > interested). > > > > Any ideas how to solve this? (As an alternative - it would be fully > > sufficient for me to use readCel if there was a method to get the > > output into an AffyBatch object.) > > > > Regards, > > Guido > > > > > > -- > Guido Steiner, PhD > F. Hoffmann-La Roche AG > PRBI-M Scientific Methods and Algorithms > Building 65/318B > CH-4070 Basel > Tel. +41 61 688 3329 > > Confidentiality Note: This message is intended only for ...{{dropped:12}} > > _______________________________________________ > 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, I can send you the file later if you want if you can't get it from Guido (since I have received it myself), but you have correctly surmised that there is a problem related to the non-existence of the DatHeader in this particular CEL file. It is not how ever true to say that the DAT header is not readily available in the AGCC CEL file, provision is made for storing it in a parental header in the file format documentation (although that is no guarantee that it will exist, the test files I had been using for affyio all had it existing). But I am sure you'd know better than I how easy that is to access via the Fusion SDK. Interestingly enough I was able to successfully read this file just fine with my installation using ReadAffy(). Only the affyio function read.celfile.header() with info="full" failed in my brief testing. Ben > Hi Guido, > > regarding affxparser: When writing a v4 CEL header, affxparser need > the DAT header, which is not readily available in AGCC CEL files so > affxparser will try to generate a valid one from what is available. > It seems like it fails in this case. I cannot say more until I see > the CEL file. Please let me (here or offline) know how I can download > this CEL file (I cannot receive attachments > 19MB). > > /Henrik > > On 10/10/07, Steiner, Guido <guido.steiner at="" roche.com=""> wrote: >> Hi, >> >> I just tried affxparser on an example CEL file from the new Affymetrix >> >> Command Console software. >> >> >> >> > library(affxparser) >> >> > convertCel("agcc.cel","gcos.cel") >> >> Error in sprintf("DatHeader=%s\n", datHeader) : zero-length argument >> >> >> >> > createCel("test.cel",header=readCelHeader("agcc.cel")) >> >> Error in sprintf("DatHeader=%s\n", datHeader) : zero-length argument >> >> >> >> So the error seems to happen at the createCell stage already. >> >> Reading the cel file with readCel does work! >> >> I have R 2.6.0/BioC 2.1 and affxparser version 1.10.0. >> >> Chip type is RAT_230 (I can provide the cel file if someone is >> >> interested). >> >> >> >> Any ideas how to solve this? (As an alternative - it would be fully >> >> sufficient for me to use readCel if there was a method to get the >> >> output into an AffyBatch object.) >> >> >> >> Regards, >> >> Guido >> >> >> >> >> >> -- >> Guido Steiner, PhD >> F. Hoffmann-La Roche AG >> PRBI-M Scientific Methods and Algorithms >> Building 65/318B >> CH-4070 Basel >> Tel. +41 61 688 3329 >> >> Confidentiality Note: This message is intended only for >> ...{{dropped:12}} >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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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Ben, just wanted to inform you that I sent the file to Henrik now. G. -----Original Message----- From: bmb@bmbolstad.com [mailto:bmb@bmbolstad.com] Sent: Thursday, October 11, 2007 7:28 PM To: Henrik Bengtsson Cc: Steiner, Guido {PRBI~Basel}; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] affxparser fails to convert AGCC format cel file Henrik, I can send you the file later if you want if you can't get it from Guido (since I have received it myself), but you have correctly surmised that there is a problem related to the non-existence of the DatHeader in this particular CEL file. It is not how ever true to say that the DAT header is not readily available in the AGCC CEL file, provision is made for storing it in a parental header in the file format documentation (although that is no guarantee that it will exist, the test files I had been using for affyio all had it existing). But I am sure you'd know better than I how easy that is to access via the Fusion SDK. Interestingly enough I was able to successfully read this file just fine with my installation using ReadAffy(). Only the affyio function read.celfile.header() with info="full" failed in my brief testing. Ben > Hi Guido, > > regarding affxparser: When writing a v4 CEL header, affxparser need > the DAT header, which is not readily available in AGCC CEL files so > affxparser will try to generate a valid one from what is available. > It seems like it fails in this case. I cannot say more until I see > the CEL file. Please let me (here or offline) know how I can download > this CEL file (I cannot receive attachments > 19MB). > > /Henrik > > On 10/10/07, Steiner, Guido <guido.steiner at="" roche.com=""> wrote: >> Hi, >> >> I just tried affxparser on an example CEL file from the new Affymetrix >> >> Command Console software. >> >> >> >> > library(affxparser) >> >> > convertCel("agcc.cel","gcos.cel") >> >> Error in sprintf("DatHeader=%s\n", datHeader) : zero-length argument >> >> >> >> > createCel("test.cel",header=readCelHeader("agcc.cel")) >> >> Error in sprintf("DatHeader=%s\n", datHeader) : zero-length argument >> >> >> >> So the error seems to happen at the createCell stage already. >> >> Reading the cel file with readCel does work! >> >> I have R 2.6.0/BioC 2.1 and affxparser version 1.10.0. >> >> Chip type is RAT_230 (I can provide the cel file if someone is >> >> interested). >> >> >> >> Any ideas how to solve this? (As an alternative - it would be fully >> >> sufficient for me to use readCel if there was a method to get the >> >> output into an AffyBatch object.) >> >> >> >> Regards, >> >> Guido >> >> >> >> >> >> -- >> Guido Steiner, PhD >> F. Hoffmann-La Roche AG >> PRBI-M Scientific Methods and Algorithms >> Building 65/318B >> CH-4070 Basel >> Tel. +41 61 688 3329 >> >> Confidentiality Note: This message is intended only for >> ...{{dropped:12}} >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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, FYI, I've just committed a bug fix to affxparser (both release and devel versions), but it will take a day or two before the builds becomes available on all platforms. Keep an eye out for affxparser v1.10.1 on http://bioconductor.org/packages/2.1/bioc/html/affxparser.html. DETAILS: The previous code relied on the fact that there was a (parent) header field 'affymetrix-dat-header' in the AGCC (Calvin) CEL header. However, in Guido's case the AGCC CEL files did not have such a field but 'affymetrix-partial-dat-header'. I've update the code to also look for this and to some tricks to create a valid old-style DAT header, which is required in the binary (v4) CEL headers. If neither exists, a more informative error message is now produced. BTW (Benilton), convertCel() will no longer generate a warning if the corresponding CDF file is not found. Cheers Henrik On 10/11/07, bmb at bmbolstad.com <bmb at="" bmbolstad.com=""> wrote: > Henrik, > > I can send you the file later if you want if you can't get it from Guido > (since I have received it myself), but you have correctly surmised that > there is a problem related to the non-existence of the DatHeader in this > particular CEL file. It is not how ever true to say that the DAT header is > not readily available in the AGCC CEL file, provision is made for storing > it in a parental header in the file format documentation (although that is > no guarantee that it will exist, the test files I had been using for > affyio all had it existing). But I am sure you'd know better than I how > easy that is to access via the Fusion SDK. > > Interestingly enough I was able to successfully read this file just fine > with my installation using ReadAffy(). Only the affyio function > read.celfile.header() with info="full" failed in my brief testing. > > > Ben > > > > > > Hi Guido, > > > > regarding affxparser: When writing a v4 CEL header, affxparser need > > the DAT header, which is not readily available in AGCC CEL files so > > affxparser will try to generate a valid one from what is available. > > It seems like it fails in this case. I cannot say more until I see > > the CEL file. Please let me (here or offline) know how I can download > > this CEL file (I cannot receive attachments > 19MB). > > > > /Henrik > > > > On 10/10/07, Steiner, Guido <guido.steiner at="" roche.com=""> wrote: > >> Hi, > >> > >> I just tried affxparser on an example CEL file from the new Affymetrix > >> > >> Command Console software. > >> > >> > >> > >> > library(affxparser) > >> > >> > convertCel("agcc.cel","gcos.cel") > >> > >> Error in sprintf("DatHeader=%s\n", datHeader) : zero-length argument > >> > >> > >> > >> > createCel("test.cel",header=readCelHeader("agcc.cel")) > >> > >> Error in sprintf("DatHeader=%s\n", datHeader) : zero-length argument > >> > >> > >> > >> So the error seems to happen at the createCell stage already. > >> > >> Reading the cel file with readCel does work! > >> > >> I have R 2.6.0/BioC 2.1 and affxparser version 1.10.0. > >> > >> Chip type is RAT_230 (I can provide the cel file if someone is > >> > >> interested). > >> > >> > >> > >> Any ideas how to solve this? (As an alternative - it would be fully > >> > >> sufficient for me to use readCel if there was a method to get the > >> > >> output into an AffyBatch object.) > >> > >> > >> > >> Regards, > >> > >> Guido > >> > >> > >> > >> > >> > >> -- > >> Guido Steiner, PhD > >> F. Hoffmann-La Roche AG > >> PRBI-M Scientific Methods and Algorithms > >> Building 65/318B > >> CH-4070 Basel > >> Tel. +41 61 688 3329 > >> > >> Confidentiality Note: This message is intended only for > >> ...{{dropped:12}} > >> > >> _______________________________________________ > >> 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 > >> > > > > _______________________________________________ > > 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, v1.10.1 works for me, too. Thanks for the fix! I can convert the CELs to the old format now and then use ReadAffy. Concerning affyio, there is still a problem leading to a crash on our system (IA64 Linux) when trying to read the Command Console format directly. (Ben is looking into this.) Best, Guido -----Original Message----- From: henrik.bengtsson@gmail.com [mailto:henrik.bengtsson@gmail.com] On Behalf Of Henrik Bengtsson Sent: Wednesday, October 17, 2007 3:31 AM To: bmb at bmbolstad.com Cc: Steiner, Guido {PRBI~Basel}; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] affxparser fails to convert AGCC format cel file Hi, FYI, I've just committed a bug fix to affxparser (both release and devel versions), but it will take a day or two before the builds becomes available on all platforms. Keep an eye out for affxparser v1.10.1 on http://bioconductor.org/packages/2.1/bioc/html/affxparser.html. DETAILS: The previous code relied on the fact that there was a (parent) header field 'affymetrix-dat-header' in the AGCC (Calvin) CEL header. However, in Guido's case the AGCC CEL files did not have such a field but 'affymetrix-partial-dat-header'. I've update the code to also look for this and to some tricks to create a valid old-style DAT header, which is required in the binary (v4) CEL headers. If neither exists, a more informative error message is now produced. BTW (Benilton), convertCel() will no longer generate a warning if the corresponding CDF file is not found. Cheers Henrik On 10/11/07, bmb at bmbolstad.com <bmb at="" bmbolstad.com=""> wrote: > Henrik, > > I can send you the file later if you want if you can't get it from Guido > (since I have received it myself), but you have correctly surmised that > there is a problem related to the non-existence of the DatHeader in this > particular CEL file. It is not how ever true to say that the DAT header is > not readily available in the AGCC CEL file, provision is made for storing > it in a parental header in the file format documentation (although that is > no guarantee that it will exist, the test files I had been using for > affyio all had it existing). But I am sure you'd know better than I how > easy that is to access via the Fusion SDK. > > Interestingly enough I was able to successfully read this file just fine > with my installation using ReadAffy(). Only the affyio function > read.celfile.header() with info="full" failed in my brief testing. > > > Ben > > > > > > Hi Guido, > > > > regarding affxparser: When writing a v4 CEL header, affxparser need > > the DAT header, which is not readily available in AGCC CEL files so > > affxparser will try to generate a valid one from what is available. > > It seems like it fails in this case. I cannot say more until I see > > the CEL file. Please let me (here or offline) know how I can download > > this CEL file (I cannot receive attachments > 19MB). > > > > /Henrik > > > > On 10/10/07, Steiner, Guido <guido.steiner at="" roche.com=""> wrote: > >> Hi, > >> > >> I just tried affxparser on an example CEL file from the new Affymetrix > >> > >> Command Console software. > >> > >> > >> > >> > library(affxparser) > >> > >> > convertCel("agcc.cel","gcos.cel") > >> > >> Error in sprintf("DatHeader=%s\n", datHeader) : zero-length argument > >> > >> > >> > >> > createCel("test.cel",header=readCelHeader("agcc.cel")) > >> > >> Error in sprintf("DatHeader=%s\n", datHeader) : zero-length argument > >> > >> > >> > >> So the error seems to happen at the createCell stage already. > >> > >> Reading the cel file with readCel does work! > >> > >> I have R 2.6.0/BioC 2.1 and affxparser version 1.10.0. > >> > >> Chip type is RAT_230 (I can provide the cel file if someone is > >> > >> interested). > >> > >> > >> > >> Any ideas how to solve this? (As an alternative - it would be fully > >> > >> sufficient for me to use readCel if there was a method to get the > >> > >> output into an AffyBatch object.) > >> > >> > >> > >> Regards, > >> > >> Guido > >> > >> > >> > >> > >> > >> -- > >> Guido Steiner, PhD > >> F. Hoffmann-La Roche AG > >> PRBI-M Scientific Methods and Algorithms > >> Building 65/318B > >> CH-4070 Basel > >> Tel. +41 61 688 3329 > >> > >> Confidentiality Note: This message is intended only for > >> ...{{dropped:12}} > >> > >> _______________________________________________ > >> 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 > >> > > > > _______________________________________________ > > 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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