Processing RAW CEL files from GEO
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PyPer ▴ 20
Last seen 9.1 years ago

Does anyone have any good resource that will provide a vignette and step by step example of how to process RAW files from GEO?

I understand that you utilize getGEOSuppFiles, untar and then readaffy()

What I don't get is why there are exp files that are zipped with the cel files.
How do I utilize these in the processing?

I've tried online to find examples, but none really talk about using the EXP files thare included in the zip. Nor are there good step by step examples.

CEL RAW geoquery readaffy • 2.2k views
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Last seen 4 months ago
United States

When researchers upload to NCBI GEO, they are pretty much free to upload any data files that they like.  GEO now pretty much requires .CEL files for Affymetrix arrays, but other files may also be included if submitted by the original researcher.  For the purposes of Affymetrix processing through Bioconductor, only the .CEL files are necessary (or useful, for that matter).  


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