Tried that, but unfortunately the email bounced. Dan James W. MacDonald wrote: > Hi Dan, > > Daniel Brewer wrote: >> After a bit more investigation I think I have tracked down an error in >> the runHomHMM code. >> >> The problem is on this line >> rownames(segList$num.states) <- paste("Chrom", unique(input$genes$Chr)) >> >> input$genes$Chr does not exist, only input$genes$Chrom. Chr gets >> created a few lines later >> colnames(segList$genes)[colnames(segList$genes) == "Chrom"] = "Chr" >> >> I have used >> update.packages(repos=biocReposList()) >> >> to get the latest package versions,but there seems to be no new version >> of snapCGH. Is there an easy way to correct this within R? How do I >> report this apparent bug? > > Send an email to the maintainer (who presumably subscribes to this list, > but I don't know if that is true of all maintainers...). > > packageDescription("snapCGH")$M > > Best, > > Jim > > > >> >> Thanks >> >> Dan >> >> Daniel Brewer wrote: >> >>> Hello, >>> >>> I am having a problem with the runHomHMM function of snapCGH. I get an >>> error which is the following: >>> >>> >>>> SegInfo.Hom <- runHomHMM(test, criteria = "AIC") >>> >>> sample is 1 Chromosomes: 1 2 3 4 5 6 7 8 9 10 11 12 13 >>> 14 15 16 17 18 19 20 21 22 >>> sample is 2 Chromosomes: 1 2 3 4 5 6 7 8 9 10 11 12 13 >>> 14 15 16 17 18 19 20 21 22 >>> Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to >>> array extent >>> >>> Does anyone know what is causing this problem or any hints on how to >>> debug it. >>> >>> The test object is produced by processCGH() and looks as follows: >>> >>> An object of class "SegList" >>> $M.observed >>> 2 3 >>> [1,] -0.04886834 -0.01567368 >>> [2,] -0.03834639 -0.27615606 >>> [3,] 0.02190425 -0.12000432 >>> [4,] 0.02654545 -0.03862101 >>> [5,] 0.24526713 0.09624987 >>> 10943 more rows ... >>> >>> $genes >>> ID Row Column ProbeUID ControlType >>> 1 1795924 56 115 5854 0 >>> 2 2862971 69 68 7165 0 >>> 3 4610962 27 92 2843 0 >>> 4 4974855 44 64 4517 0 >>> 5 2258165 45 55 4639 0 >>> >>> >>> SystematicName Description Block Spot.Number Feature.Name Chr ChrStart >>> 1 AAC67502 pSPORT 1 8695 AAC67502 1 939866 >>> 2 AI739106 pINCY 1 10676 AI739106 1 989430 >>> 3 AF016903 pINCY 1 4148 AF016903 1 1021843 >>> 4 AF148950 pINCY 1 6772 AF148950 1 1039517 >>> 5 AF296658 pSPORT 1 6919 AF296658 1 1230203 >>> ChrEnd Position >>> 1 941129 0.939866 >>> 2 989975 0.989430 >>> 3 1022260 1.021843 >>> 4 1041741 1.039517 >>> 5 1230592 1.230203 >>> 10943 more rows ... >>> >>> $design >>> [1] -1 -1 >>> >>> >>> Many thanks >>> >>> Daniel >>> >> >> > > -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis MUCRC 15 Cotswold Road Sutton, Surrey SM2 5NG United Kingdom Tel: +44 (0) 20 8722 4109 Fax: +44 (0) 20 8722 4141 Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addre...{{dropped}}