Processing RAW CEL files from GEO
1
1
Entering edit mode
PyPer ▴ 20
@pyper-6819
Last seen 6.7 years ago
Australia

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 • 1.7k views
ADD COMMENT
2
Entering edit mode
@sean-davis-490
Last seen 18 days 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).  

ADD COMMENT

Login before adding your answer.

Traffic: 374 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6