Hi list ! I am using the exonmap package. I did every steps and I now have a list of genes that have at least on significant differential expressed exon (sigs.exon) I want to calculate the splicing index as explained but it looks like the computer enters a loop and jam there. I come back and everytime it's killed. I use a common computer (32Gb RAM 64bit massive machine) Here is the function I used > si.sigs <- si(rma.data, sigs.gene, "group", c("a","b")) where rma.data is the output of the RMA I ran before limma (length sigs.gene is the output of the probeset.to.gene function on the limma filtered significant list. (length 22 000) Any ideas ? Thanks ! Mathieu McGill University Dept. Neurology and Neurosurgery Dept. Bioinformatics [[alternative HTML version deleted]]