[BioC] How to create customized probe package for GCRMA?
kzhang at arep.med.harvard.edu
Wed May 12 02:08:13 CEST 2004
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
Email: kzhang at genetics.med.harvard.edu
More information about the Bioconductor