Thanks Mike, that seems exactly the case. Does it mean I have to re-run both the reads counting and computation? or can I fix it somehow? thanks, Francesco On 6 Aug 2012, at 23:46, Mike Love > wrote: On Tue, Aug 7, 2012 at 12:11 AM, Lescai, Francesco > wrote: Hi there, I'm having an error in exomeCopy when I count the CNVs. No previous error in any of the other steps illustrated in the vignette the computation of the fit list didn't give any warning and it seems to be formatted correctly > fit.list[[1]][1] $`1` ExomeCopy object sample name: UCLG_502_ATCACG_L003 percent normal state: 79.87% > summary(fit.list$UCLG_502_ATCACG_L003$`1`) Length Class Mode 1 ExomeCopy S4 but then I get > compiled.segments <- compileCopyCountSegments(fit.list) Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : solving row 1: negative widths are not allowed Hi Francesco, I have seen this error before when the target GRanges has duplicate or unsorted regions, and fixed this in the devel branch. You could try to reduce the target GRanges first, before counting sample read counts. Could you try: all.equal(target, reduce(target)) If these are in fact equal, you can send me the fit.list object and I can try to debug. best, Mike --------------------------------------------------------------------------------- Francesco Lescai, PhD, EDBT Senior Research Associate in Genome Analysis University College London Faculty of Population Health Sciences Dept. Genes, Development & Disease ICH - Molecular Medicine Unit, GOSgene team 30 Guilford Street WC1N 1EH London UK email: f.lescai@ucl.ac.uk phone: +44.(0)207.905.2274 [ext: 2274] -------------------------------------------------------------------------------- [[alternative HTML version deleted]]