Hi John, This appears to be a bug for fitted objects which have no predicted variants (as the show command gives "percent normal state: 100%"). I will fix it. best, Mike > > ----- Forwarded Message ----- > From: John linux-user <johnlinuxuser at="" yahoo.com=""> > To: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> > Sent: Sunday, March 18, 2012 1:54 PM > Subject: [BioC] copyCountSegments(fit) failed exomeCopy > > Hello > > I tried to the copyCountSegments from exomeCopy, but it failed as shown > below. It complained negative width, but I table the width value, and have > never found any negative value in width column for range objects. Could any > one give some suggestions? Thanks. > > John > > >> fit <- exomeCopy(exomecounts["chr1"],sample.name="HGPIPE_6159", > +??????????????????? X.names=c("bg","GC","GC.sq","width"),S=0:6,d=2) >>?? show(fit) > > ExomeCopy object > type: exomeCopy > percent normal state: 100% >> copyCountSegments(fit) > Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") > : > ? solving row 1: negative widths are not allowed > >> sessionInfo() > R version 2.14.2 (2012-02-29) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > ?[1] LC_CTYPE=en_US.UTF-8?????? LC_NUMERIC=C????????????? > ?[3] LC_TIME=en_US.UTF-8??????? LC_COLLATE=en_US.UTF-8??? > ?[5] LC_MONETARY=en_US.UTF-8??? LC_MESSAGES=en_US.UTF-8?? > ?[7] LC_PAPER=C???????????????? LC_NAME=C???????????????? > ?[9] LC_ADDRESS=C?????????????? LC_TELEPHONE=C??????????? > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C?????? > > attached base packages: > [1] stats???? graphics? grDevices utils???? datasets? methods?? base???? > > other attached packages: > [1] exomeCopy_1.0.2???? Rsamtools_1.6.3???? Biostrings_2.22.0? > [4] GenomicRanges_1.6.7 IRanges_1.12.6????? foreign_0.8-49???? > > loaded via a namespace (and not attached): > [1] bitops_1.0-4.1???? BSgenome_1.22.0??? RCurl_1.91-1?????? > rtracklayer_1.14.4 > [5] tools_2.14.2?????? XML_3.9-4????????? zlibbioc_1.0.1??? >> > ??? [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor