[BioC] calling aberrations after segmentation with \"copynumber\" package

[Gabriele Zoppoli [guest]]

Dear Bioconductor mailing list,

after segmenting my samples (Agilent 4x180k aCGH arrays) with the package copynumber, I see there are options to empirically determine a threshold for gains and losses.

Does anybody have any suggestion on how to do that by applying an algorithm such EM used in CGHCall?

Thanks in advance

Gabriele

 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=de_BE.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=de_BE.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=de_BE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_BE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] copynumber_1.1.1   BiocGenerics_0.6.0

loaded via a namespace (and not attached):
[1] GenomicRanges_1.12.5 IRanges_1.18.4       stats4_3.0.2        
[4] tools_3.0.2     

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