I have been trying to use UPC_Generic_ExpressionSet function from the SCAN UPC package with Human Exon Array dataset and was stuck at a point. I want to use UPC based detection and correct for GC content but the sequence file for Affymetrix is at probe level whereas I am using alternative exon array mappings from BrainArray. Thus the expressionset contains SCAN normalised intensities at exon level. In this case do I need to supply information about sequence of each exon? If not then how should I approach this when using alternate mappings?