

Hello, 

I am using R 2.10.0. The sessionInfo data is below at the end
of this message. I am using Ubuntu 10.04. 

I am attempting to re-annotate
custom Affy PM-only chip using a new gene-annotation for my prokaryotic
genome. I have gotten stuck on altcdfenvs, however. 

What I have done so
far: 

1. Changed the makeProbePackage code to not require MM probe data


2. Created a probe package from my probe_tab file with makeProbePackage
(for some reason 4800 probes did not match between the probe_tab file and
the Affy-supplied .CDF file) 

3. Installed the new probe package with help
from James MacDonald 

4. Started following the altcdfenvs
documentation....selected the constituting elemets, matched the probes....
Everything went smoothly until match analysis: 

> alt.cdf 
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