[BioC] How to create customized probe package for GCRMA?

[Kun Zhang]

Hello!

I'm trying to use the GCRMA package for a set of Affy E. Coli chip data. My 
experiments were done in a "non-conventional" way, in which I  hybridized 
genomic DNA with gene expression chip in order to detect copy number 
changes on the DNA level instead of gene expression level. So throughout my 
analysis, I replaced the standard CDF file with a customized file I created 
by my own. It works okay with all methods in the affy package, but when I 
tried the GCRMA package,  I got an error saying that a probepackage is 
missing. I would like to know how to create a customized probe package for 
this purpose. Can I do it with the makecdfenv package? What's the format of 
the probe file? Thank you!

Kun Zhang, Ph. D.
Post-doctoral Associate, The Church Lab
Department of Genetics
Harvard Medical School
77 Avenue Louis Pasteur, NRB-238
Boston, MA 02115
Phone: 617-432-6219
Email: kzhang at genetics.med.harvard.edu