I've been trying to use FIRMA analysis 
(http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis) on my 
mouse arrays (
Mouse Exon 1.0 ST Array - 

It looks like the scripts have completed successfully, but I have a few 
1) How can I figure out which genes/exons correspond with the "unitName" 
and "groupName" fields returned by "extractDataFrame(fs, addNames=TRUE)"?  

implies that I can download a "NetAffx tabular text files" from Ayymetrix 
and use that. However, I cannot get Affymetrix to provide me with a login 
to get that file. I hoped that I could load ‘MoEx-1_0-st-v1,HB20100926.acs’ 
and use that to get enough probe information to reconstruct the names using 
annmap, but I cannot figure out how to load the .acs file.

2) How do I run FIRMA after I change the tags?
I switch from 'MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf' to 
'MoEx-1_0-st-v1,U-Ensembl50,G-Affy,EP.cdf' in the hope that the Ensemble 
file would have easier to interpret names.  However, after rerunning my 
analysis script, it looks like aroma is reading things from intermediate 
files.  I get the error message:
*Error: Cannot set CDF. The specified CDF structure 
('MoEx-1_0-st-v1,U-Ensembl50,G-Affy,EP,monocell') is not compatible with 
the chip type ('MoEx-1_0-st-v1,coreR1,A20080718,MR,monocell') of the CEL 
file. The number of cells do not match: 279841 != 224202*

I know that FIRMA dumps many intermediate files, but I would prefer not to 
delete things at random in the hope that something will eventually work.

3) How can I update the .cdf files?
I would like to use the brainarray .cdf files 
because they are regularly updated.  However, (based on the results of the 
FIRMA run) their .cdf files do not have the correct exon/gene annotations. 
 I can figure out which exons should be paired with which genes from 
annmap, but I cannot figure out how to store this information in the .cdf 

Thank you,

When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.

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