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 
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 
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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