Dear Gunter, I am wondering if there is a limit on the number of tumor-normal pairs that referencecn.mops() can handle because whenever I give it more than 2 pairs, I get an error saying "subscript out of bounds". Below is how you can reproduce the error using data provided by cn.mops Let's say XRanges[,1:4] are tumor samples and the corresponding normal samples are XRanges[,5:8] > data(cn.mops) resRef2 <- referencecn.mops (XRanges[,1:2], XRanges[,5:6]) Normalizing... Starting local modeling, please be patient... Reference sequence: chrA Starting segmentation algorithm... Using "fastseg" for segmentation. > resRef3 <- referencecn.mops (XRanges[,1:4], XRanges[,5:8]) Normalizing... Error in XR.norm[, (N + 1):(N * M), drop = FALSE] : subscript out of bounds Looking forward to your feedback! Thanks for the great work! Johnbosco -- 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, Thanks again for reporting the issues. They have been solved and I have uploaded the new versions of the function "referencecn.mops" of the package cn.mops (both release and devel) to Bioconductor. The new version will appear on Bioconductor within the next days. Meanwhile you can download the source packages from http://www.bioinf.jku.at/software/cnmops/ Do not hesitate to contact me, if you encounter any further problems. Regards, G?nter On 02/08/2014 01:44 PM, Johnbosco [guest] wrote: > Dear Gunter, > I am wondering if there is a limit on the number of tumor-normal pairs that referencecn.mops() can handle because whenever I give it more than 2 pairs, I get an error saying "subscript out of bounds". Below is how you can reproduce the error using data provided by cn.mops > > Let's say XRanges[,1:4] are tumor samples and the corresponding normal samples are XRanges[,5:8] > >> data(cn.mops) > resRef2 <- referencecn.mops (XRanges[,1:2], XRanges[,5:6]) > Normalizing... > Starting local modeling, please be patient... > Reference sequence: chrA > Starting segmentation algorithm... > Using "fastseg" for segmentation. > >> resRef3 <- referencecn.mops (XRanges[,1:4], XRanges[,5:8]) > Normalizing... > Error in XR.norm[, (N + 1):(N * M), drop = FALSE] : > subscript out of bounds > > Looking forward to your feedback! > > Thanks for the great work! > > Johnbosco > > > -- 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. -- G?nter Klambauer Institute of Bioinformatics Johannes Kepler University, Linz, Austria http://www.bioinf.jku.at/people/klambauer/