Hi, about the error with convertCel() of affxparser: would you mind sending me (not via this list) a CEL file that causes that error so I could troubleshoot this further. /Henrik (coauthor of affxparser) On Tue, Feb 22, 2011 at 12:13 PM, Wendy Qiao <wendy2.qiao at="" gmail.com=""> wrote: > Hi all, I need to load and normalize CEL files from two different platforms, one platform is *U133AAofAv2 (22944 affyids)* and the other is *HG-U133A_2 (22277 affyids)*. I believe that these two platforms have very similar annotations. When I read all the file together using ReadAffy, I got an error saying, > es.affy<-ReadAffy(filenames=celfile, celfile.path=celpath, phenoData=NULL) Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData, ? Cel file XX does not seem to have the correct dimensions I figure that is because two platform has different cdf. So I tried to change the cdf name for *U133AAofAv2 *using library("affxparser"). The I got the following errors, > convertCel(celfile, celfile.output, newChipType="HG-U133A_2") Error in .unwrapDatHeaderString(header$DatHeader) : ? Internal error: Failed to extract 'pixelRange' and 'sampleName' from DAT header. ?They became identical: ? HG-U133A_2.1sq ?I am not sure how to get around with this problem? Could anybody helps? Or what would be the best way to normalize two datasets like mine? Thank you very much. Any suggestion is appreciated. Thank you very much, Wendy [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

On Tue, Feb 22, 2011 at 2:15 PM, Henrik Bengtsson <hb at="" biostat.ucsf.edu=""> wrote: > Hi, > > about the error with convertCel() of affxparser: would you mind > sending me (not via this list) a CEL file that causes that error so I > could troubleshoot this further. It turns out that for the particular CEL file that triggered the error: Internal error: Failed to extract 'pixelRange' and 'sampleName' from DAT header. ?They became identical: ... for convertCel() had a CEL file header containing a nearly empty DAT header (which I have never seen before). This had nothing to do with using the 'newChipType' argument; the same error also occurred when doing: convertCel(pathname, pathnameNew) I've updated the code so that it is more forgiving on such DAT headers in CEL files. The update is/will be available in affxparser v1.23.3 recently committed to the BioC *devel* branch. When the devel branch have undergone enough real-world testing, this update ("bug fix") will probably also be added to the *release* version of the package. /Henrik PS. As I just replied to in the original BioC-thread 'load and normalize arrays from different platform', it is not correct (=very wrong!) to change the chip type label of a 'U133AAofAv2' CEL file to 'HG-U133A_2'. They are simply not for the same physical chip type design. I've added a section to help(convertCel) warning about such misuse. > > /Henrik > (coauthor of affxparser) > > On Tue, Feb 22, 2011 at 12:13 PM, Wendy Qiao <wendy2.qiao at="" gmail.com=""> wrote: >> Hi all, I need to load and normalize CEL files from two different platforms, one platform is *U133AAofAv2 (22944 affyids)* and the other is *HG-U133A_2 (22277 affyids)*. I believe that these two platforms have very similar annotations. When I read all the file together using ReadAffy, I got an error saying, > es.affy<-ReadAffy(filenames=celfile, celfile.path=celpath, phenoData=NULL) Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData, ? Cel file XX does not seem to have the correct dimensions I figure that is because two platform has different cdf. So I tried to change the cdf name for *U133AAofAv2 *using library("affxparser"). The I got the following errors, > convertCel(celfile, celfile.output, newChipType="HG-U133A_2") Error in .unwrapDatHeaderString(header$DatHeader) : ? Internal error: Failed to extract 'pixelRange' and 'sampleName' from DAT header. ?They became identical: ? HG-U133A_2.1sq ?I am not sure how to get around with this problem? Could anybody helps? Or what would be the best way to normalize two datasets like mine? Thank you very much. Any suggestion is appreciated. Thank you very much, Wendy [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >