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@genetics.med.harvard.edu