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

Gabriele Zoppoli [guest] guest at bioconductor.org
Wed Jan 29 16:43:26 CET 2014

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


 -- output of sessionInfo(): 

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

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=de_BE.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=de_BE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=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     

Sent via the guest posting facility at bioconductor.org.

More information about the Bioconductor mailing list