I added my exon library files to my library folder but the application still will not analyze exon arrays.
Examination of the messages in the status window should identify the specific library files that the Expression Console software is missing. If the computer is connected to the internet, the easiest solution is to use the download library files functionality to add the necessary files. In addition to the"pgf, clf, and bgp" files, the Expression Console software requires two additional files for exon analysis: the "qcc" file with control probe information, and an "exon_analysis_configuration" file. These files are automatically included when the Expression Console software is used to download the library files, but if you are manually adding files to the Expression Console software, they need to be obtained from Affymetrix.com.