Can I use Bioconductor to parse *.chp (Affymetrix) files?
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Anton Kratz ▴ 10
@anton-kratz-4240
Last seen 9.6 years ago
Hi, I have a bunch of Affymetrix *.chp files in binary format. I do not have access to Affymetrix software for working with this and I want to do subsequent analysis of this data with my own scripts anyway. Can I use Bioconductor to convert such binary *.chp files into human-readable cleartext (f.e. tab-delimited table)? Or otherwise parse them? My goal would be a file with genes (not probes) and their expression values. As I understand it, normalization, summarization etc has already been done and is somewhere in the *.chp files, but I don't see a way to get the data. I figured out that Bioconductor let's me work with *.cel files using the affy package, but what about *.chp?! Thanks. Anton [[alternative HTML version deleted]]
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@james-w-macdonald-5106
Last seen 11 hours ago
United States
Hi Anton, On 8/30/2010 6:25 AM, Anton Kratz wrote: > Hi, > > I have a bunch of Affymetrix *.chp files in binary format. I do not have > access to Affymetrix software for working with this and I want to do > subsequent analysis of this data with my own scripts anyway. > > Can I use Bioconductor to convert such binary *.chp files into > human-readable cleartext (f.e. tab-delimited table)? Or otherwise parse > them? > > My goal would be a file with genes (not probes) and their expression values. > As I understand it, normalization, summarization etc has already been done > and is somewhere in the *.chp files, but I don't see a way to get the data. > > I figured out that Bioconductor let's me work with *.cel files using the > affy package, but what about *.chp?! Yup. See readChp() in the affxparser package. Best, Jim > > Thanks. > > Anton > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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