I used getSegmentReadCountsFromBAM() to get a GRanges object from a list of tumor-normal bam files Then I used referencecn.mops(). Whenever I try to calculate integer copy numbers using calcIntegerCopyNumbers() I get an error. This error can be reproduced using the data provided by cn.mops so this might be a bug? >data(cn.mops) >resRef2 <- referencecn.mops (XRanges[,1], XRanges[,2]) Normalizing... Starting local modeling, please be patient... Reference sequence: chrA Starting segmentation algorithm... Using "fastseg" for segmentation. > resRef5 <- calcIntegerCopyNumbers(resRef2) Error in `colnames<-`(`*tmp*`, value = "S_1") : length of 'dimnames' [2] not equal to array extent -- output of sessionInfo(): R version 3.0.2 (2013-09-25) Platform: x86_64-redhat-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=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] snow_0.3-13 cn.mops_1.8.3 GenomicRanges_1.14.4 [4] XVector_0.2.0 IRanges_1.20.6 Biobase_2.22.0 [7] BiocGenerics_0.8.0 BiocInstaller_1.12.0 loaded via a namespace (and not attached): [1] Biostrings_2.30.1 bitops_1.0-6 Rsamtools_1.14.2 stats4_3.0.2 [5] tools_3.0.2 zlibbioc_1.8.0 -- Sent via the guest posting facility at bioconductor.org.

Dear Johnbosco Taybewa, Thank you for reporting this problem. We are already working on fixing it in the next version which will be released within the next days(probably 10th Feb). Best regards, Günter Klambauer On 02/07/2014 05:11 PM, Johnbosco [guest] wrote: > I used getSegmentReadCountsFromBAM() to get a GRanges object from a list of tumor-normal bam files > Then I used referencecn.mops(). Whenever I try to calculate integer copy numbers using calcIntegerCopyNumbers() I get an error. This error can be reproduced using the data provided by cn.mops so this might be a bug? > >> data(cn.mops) >> resRef2 <- referencecn.mops (XRanges[,1], XRanges[,2]) > Normalizing... > Starting local modeling, please be patient... > Reference sequence: chrA > Starting segmentation algorithm... > Using "fastseg" for segmentation. >> resRef5 <- calcIntegerCopyNumbers(resRef2) > Error in `colnames<-`(`*tmp*`, value = "S_1") : > length of 'dimnames' [2] not equal to array extent > > -- output of sessionInfo(): > > R version 3.0.2 (2013-09-25) > Platform: x86_64-redhat-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=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] snow_0.3-13 cn.mops_1.8.3 GenomicRanges_1.14.4 > [4] XVector_0.2.0 IRanges_1.20.6 Biobase_2.22.0 > [7] BiocGenerics_0.8.0 BiocInstaller_1.12.0 > > loaded via a namespace (and not attached): > [1] Biostrings_2.30.1 bitops_1.0-6 Rsamtools_1.14.2 stats4_3.0.2 > [5] tools_3.0.2 zlibbioc_1.8.0 > > -- > Sent via the guest posting facility at bioconductor.org. -- Günter Klambauer Institute of Bioinformatics Johannes Kepler University, Linz, Austria http://www.bioinf.jku.at/people/klambauer/ [[alternative HTML version deleted]]