Hi, Recently I am performing an array experiment and want to compare my results with those deposited into GEO. I had some trouble in running gcrma on some of the data seriers (such as GSE3751),mainly because I could not make a probe package for the GNF1-M custom affy chip in R. I made the GPL1073cdf package by myself, but the GPL1073 platform files (GPL1073.probe) is not readily recognized by the makeProbePackage function in the AnnotationDbi package (Matchprobes is deprecated).Seems it requires a particular probe tabular file format that is not same as provided by GPL1073.probe. Could anyone help me out to convert the GPL1073.probe to a file with format recognizable to makeProbePackage? I am really stuck at this step. Thanks a lot. Xiaodong Li Wuhan University

Hi Xiadong, Not really an answer to your question, but it may be relevant to know that Manhong Dai and Fan Meng from the MBNI provide remapped, current CDFs in various flavors for this array as well. These remappings include a probe file (R-package) that can be used for ao gcrma. Check e.g. here for RefSeq-based definitions: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/13. 0.0/refseq.asp Regards, Guido ------------------------------------------------ Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email:????? guido.hooiveld at wur.nl internet:?? http://nutrigene.4t.com http://www.researcherid.com/rid/F-4912-2010 -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of ??? Sent: Monday, February 07, 2011 09:32 To: bioconductor at r-project.org Subject: [BioC] How to make a probe package with the GPL1073.probe file from GEO. Hi, Recently I am performing an array experiment and want to compare my results with those deposited into GEO. I had some trouble in running gcrma on some of the data seriers (such as GSE3751),mainly because I could not make a probe package for the GNF1-M custom affy chip in R. I made the GPL1073cdf package by myself, but the GPL1073 platform files (GPL1073.probe) is not readily recognized by the makeProbePackage function in the AnnotationDbi package (Matchprobes is deprecated).Seems it requires a particular probe tabular file format that is not same as provided by GPL1073.probe. Could anyone help me out to convert the GPL1073.probe to a file with format recognizable to makeProbePackage? I am really stuck at this step. Thanks a lot. Xiaodong Li Wuhan University _______________________________________________ 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