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.
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