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Question: Processing RAW CEL files from GEO
1
gravatar for PyPer
3.1 years ago by
PyPer20
Australia
PyPer20 wrote:

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.

ADD COMMENTlink modified 3.1 years ago by Sean Davis21k • written 3.1 years ago by PyPer20
2
gravatar for Sean Davis
3.1 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:

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).  

ADD COMMENTlink written 3.1 years ago by Sean Davis21k
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