Hi everyone,

I am working on Affymetrix Human Exon Arrays and in order to perform an 
analysis on every possible exon on the array, I would like to use the 
"fullR3" CDF (see 
http://www.aroma-project.org/chipTypes/HuEx-1_0-st-v2/transcriptClustersCDFs
).
Now, I just came across a thread stating that it makes more sense to use 
core probes instead in order to derive true gene expression levels (see 
http://www.mail-archive.com/aroma-affymetrix@googlegroups.com/msg01571.html). 
In my opinion this limits the overall discovery rate, since a number of 
genes is not included in the core annotation and thereby missed completely. 
Thus, I was wondering whether it is possible to estimate the gene 
expression level via core or extended probes and then calculate the 
deviation/FIRMA scores for full probes as well.

Best regards

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