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!
>
>
>
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-- 
Matthew N McCall, PhD
112 Arvine Heights
Rochester, NY 14611
Cell: 202-222-5880



      
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