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Kun Zhang
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10
@kun-zhang-759
Last seen 10.4 years ago
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