Hello, all: I have 16 exon arrays from 4 groups, A1, A2 and B1, B2. As are genetically identical but with different treatment,Bs are genetically identical (but different from As) with different treatment 1 and 2. I am interested in finding alternative splicing events that was affected by treatment on A and B and also by genetics (under same treatement). Therefore, the comparison I am interested are A1 vs. A2, B1vsB2, A1 vs B1 (only treatment 1) . My question is, when I do RMA and calculate the FIRMA score, do I use all 16 array I have to get Firma scores, then use limma as suggested before to apply to design matrix and contrast matrix? Or should I for each comparison , do RMA and FIRMA score for exon arrays only involved in that comparison? Thanks for your input!
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