Example of a set of exon skipping events and exon-skipping cleaning procedure. A) Example of a set of exon skipping events. The gene-level probe set (gene) G1 is made of 5 exon-level probe sets (exons) E1, E2, E3, E4, E5. Exon-level probe set signals associated with 128 pM spike-in are black whereas signals associated with 32 pM spike-in are grey. New genes are created combining exon-level expressions derived from different spike-in concentrations. In this specific case, the combination of 128 and 32 pM spike-in signals for gene G1 are used for the generation of 5 new genes (G1skipE1, G1skipE2, etc) each one characterized by a skipping event, given by the spike-in at 32 pM, in one of the 5 exons of gene G1. The unspliced exons are instead given by the 128 pM spike-in. For the sake of simplicity only one out of the three technical replicates is shown. B) Exon-skipping cleaning procedure. The cleaning procedure, applied to all new genes characterized by a skipping event, retains only those where the synthetic skipping event represents the smallest intensity or SI value within the exons belonging to the gene. Here, it is shown the example of gene G5, which is made of 7 exons and therefore produces 7 new genes, G5skipE1, G5skipE2, etc. In G5skipE3 gene, exon E3 should be the only exon characterized by the smallest SI. G5skipE3 gene is retained in the set 128-32, since E3 (grey) is characterized by the smallest SI within all 7 exons (black). The gene is instead removed in the set 2-0 since exon E5 has a SI smaller than the one of exon E3.