[BioC] Creating Affymetrix CDF files

Srinivas Iyyer srini_iyyer_bio at yahoo.com
Mon Jan 19 21:50:22 CET 2009


What is a CDF file and what should be the contents of it (format) and how should I make it. 

My question is:
I have a probe, its coordinates and annotation in tab delim file. 

Prob X cord <tab> Prob Y cord <tab> type (PM) <tab> pbset name <tab> annotations

I have this for u95av2. 

Now I want to run RMA on on u95av2 chip cel files using my probeset definitions. I removed probes that are not part of sequence and many more. 

is there a step-wise protocol to make read.celfiles and rma functions understand my definition file. 

Please help. 
thank you

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