Hello, I have some data that I'm segmenting with DNAcopy and the processing enters an infinite loop when it gets to chr13. It's worked for me previously on other datasets, so this could be one of those problems that is hard to track down because it only happens on a certain dataset. But I am hopeful that the maintainer might have the intuition and experience to uncover the cause of it. Here is a minimal and reproducible example : library(DNAcopy) download.file("http://129.94.136.7/file_dump/dario/CNobjects.RData", "./CNobjects.RData") # 3.2 MB load("CNobjects.RData") # objects 'cn' and 'wts' segment(cn, weights = wts, verbose = 3) My session is : R version 2.13.0 (2011-04-13) Platform: x86_64-unknown-linux-gnu (64-bit) attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] DNAcopy_1.26.0 loaded via a namespace (and not attached): [1] tools_2.13.0 -------------------------------------- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia

There is something weird in your data set. Of the 154005 values there are 137109 unique ones. Oddly there are 16335 that have the same value. > table(table(cn$Fold.Change)) 1 2 3 4 5 9 16335 135779 883 31 3 1 1 1 Those 16335 repeated values give several contiguous stretches of duplicated values, some very long (a stretch of 921 at the start of chr13), which are bypassing various sanity checks in the code. Venkat On 6/23/11 1:00 AM, "Dario Strbenac" <d.strbenac at="" garvan.org.au=""> wrote: > Hello, > > I have some data that I'm segmenting with DNAcopy and the processing enters an > infinite loop when it gets to chr13. It's worked for me previously on other > datasets, so this could be one of those problems that is hard to track down > because it only happens on a certain dataset. But I am hopeful that the > maintainer might have the intuition and experience to uncover the cause of it. > > Here is a minimal and reproducible example : > > library(DNAcopy) > download.file("http://129.94.136.7/file_dump/dario/CNobjects.RData", > "./CNobjects.RData") # 3.2 MB > load("CNobjects.RData") # objects 'cn' and 'wts' > segment(cn, weights = wts, verbose = 3) > > My session is : > > R version 2.13.0 (2011-04-13) > Platform: x86_64-unknown-linux-gnu (64-bit) > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] DNAcopy_1.26.0 > > loaded via a namespace (and not attached): > [1] tools_2.13.0 > > > -------------------------------------- > Dario Strbenac > Research Assistant > Cancer Epigenetics > Garvan Institute of Medical Research > Darlinghurst NSW 2010 > Australia > -- Venkatraman E. Seshan, Ph.D. | Attending Biostatistician Director of Biostatistics Computer-Intensive Support Services Department of Epidemiology and Biostatistics | MSKCC 307 E 63rd St 3rd Floor | New York, NY 10065 Phone: 646-735-8126 | Fax: 646-735-0010 ===================================================================== Please note that this e-mail and any files transmitted with it may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer.