convert affy CEL files to data.frame??
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@d-m-4384
Last seen 7.0 years ago
Hi Does anyone know how to convert the binary data in an affymetrix .CEL file via data.frame or any other way?  The way i normally convert to a data frame doesn't seem to work here. I was to see the raw data from my arrays, but not the grouped probeset data. I trawled the net, tried numerous commands and i dont think the Affymetirix Expression Console Software does it for the raw data. Alternatively, how can i log2 the .CEL file data.  I want to present it as a heatmap. Cheers! [[alternative HTML version deleted]]
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@matthew-mccall-4459
Last seen 2.3 years ago
United States
Does the following do what you want? library(affy) setwd(<where your="" cel="" files="" are="">) obj=ReadAffy(filenames=<your cel="" file="" names="">) pms=log2(pm(obj)) pms now contains the log2 expression values for the perfect match (pm) probes. Matt On Wed, Feb 2, 2011 at 12:54 PM, D M <srafmonkey at="" yahoo.co.uk=""> wrote: > Hi > > Does anyone know how to convert the binary data in an affymetrix .CEL file via data.frame or any other way?? The way i normally convert to a data frame doesn't seem to work here. > > I was to see the raw data from my arrays, but not the grouped probeset data. > > I trawled the net, tried numerous commands and i dont think the Affymetirix Expression Console Software does it for the raw data. > > Alternatively, how can i log2 the .CEL file data.? I want to present it as a heatmap. > > Cheers! > > > > ? ? ? ?[[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 > -- Matthew N McCall, PhD 112 Arvine Heights Rochester, NY 14611 Cell: 202-222-5880
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Yes, that works wonderfully!� Thank you! --- On Wed, 2/2/11, Matthew McCall <mccallm@gmail.com> wrote: From: Matthew McCall <mccallm@gmail.com> Subject: Re: [BioC] convert affy CEL files to data.frame?? To: "D M" <srafmonkey@yahoo.co.uk> Cc: Bioconductor@r-project.org Date: Wednesday, 2 February, 2011, 18:04 Does the following do what you want? library(affy) setwd(<where your="" cel="" files="" are="">) obj=ReadAffy(filenames=<your cel="" file="" names="">) pms=log2(pm(obj)) pms now contains the log2 expression values for the perfect match (pm) probes. Matt On Wed, Feb 2, 2011 at 12:54 PM, D M <srafmonkey@yahoo.co.uk> wrote: > Hi > > Does anyone know how to convert the binary data in an affymetrix .CEL file via data.frame or any other way?� The way i normally convert to a data frame doesn't seem to work here. > > I was to see the raw data from my arrays, but not the grouped probeset data. > > I trawled the net, tried numerous commands and i dont think the Affymetirix Expression Console Software does it for the raw data. > > Alternatively, how can i log2 the .CEL file data.� I want to present it as a heatmap. > > Cheers! > > > > � � � �[[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Matthew N McCall, PhD 112 Arvine Heights Rochester, NY 14611 Cell: 202-222-5880 [[alternative HTML version deleted]]
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@giuliogenovese-17235
Last seen 3.0 years ago

I wrote affy2vcf, a bcftools plugin that is capable of generating VCF files out of the output of the Affymetrix apt-probeset-genotype command line tool.

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