Hi, all: I am working on Affy Mouse Exon Array . Because of the experiment design and quality of the hybridization, we have two arrays hybridized from one mouse (same biological sample). I assume that I should treat these two arrays as tehcnical duplicates. If that is the case, I could do background correction, normalization and summary separately for these two arrays,(RMA, and ExonRmaPlm), then before I use FIRMA to get firma scores, can I just do average on plm of these two arrays? But then what do I feed in FIRMAModel? ( The default one is just plm results directly from ExonRmaPlm) .Or any suggestions about how to deal with this situation? My goal is to find novel splicing events, but right now I am just using core annotation to try it out. Thanks!
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