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.
>
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-- 
Günter Klambauer
Institute of Bioinformatics
Johannes Kepler University, Linz, Austria
http://www.bioinf.jku.at/people/klambauer/


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