[BioC] referencecn.mops: limit on number of tumor-normal pairs?

[Johnbosco [guest]]

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 

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