referencecn.mops: workaround
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Entering edit mode
@gunter-klambauer-5426
Last seen 20 months ago
Austria
Hello Johnbosco, Thank you for reporting this issue! We are already working on taking your requirement into account in the next version which will be released within the next days. In the meantime, we suggest to use the following workaround: library(cn.mops) data(cn.mops) X.norm <-normalizeGenome(XRanges) resRef3 <- referencecn.mops (X.norm[,1:4], X.norm[,5:8],norm=FALSE) Best regards, Günter -- Günter Klambauer Institute of Bioinformatics Johannes Kepler University, Linz, Austria http://www.bioinf.jku.at/people/klambauer/ 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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Günter Klambauer Institute of Bioinformatics Johannes Kepler University, Linz, Austria http://www.bioinf.jku.at/people/klambauer/ [[alternative HTML version deleted]]
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