[BioC] CGHCall problems

Bernard North [guest] guest at bioconductor.org
Tue Aug 6 18:12:05 CEST 2013

Dear All,

I am using CGHcall to segment and call aCGH copy number data.
My understanding is that the segmentation step of CGHcall is the same CBS method used in DNAcopy.
CGHcall has a function called "calls" which has segments as rows (defined as start probe to end probe) and columns for each sample with the elements being calls.
Given that DNAcopy has a different segmentation for each sample how is the segmentation in allcalls decided upon ?
Calls is run as allcalls<-data.frame(calls(result)) where result is the final CGHCall object as per the vignette

Also does CGHcall provide pvalues or qvalues to test if any regions are recurrently amplified or deleted over samples ?

 -- output of sessionInfo(): 

> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-redhat-linux-gnu (64-bit)

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

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

other attached packages:
 [1] CGHcall_2.18.0     snowfall_1.84-4    snow_0.3-12        CGHbase_1.18.0    
 [5] marray_1.36.0      impute_1.32.0      GEOquery_2.24.1    Biobase_2.18.0    
 [9] BiocGenerics_0.4.0 snapCGH_1.28.0     limma_3.14.4       DNAcopy_1.32.0    

loaded via a namespace (and not attached):
 [1] aCGH_1.36.0           affy_1.36.1           affyio_1.26.0        
 [4] annotate_1.36.0       AnnotationDbi_1.20.7  BiocInstaller_1.8.3  
 [7] cluster_1.14.3        DBI_0.2-7             genefilter_1.40.0    
[10] GLAD_2.20.0           grid_2.15.2           IRanges_1.16.6       
[13] lattice_0.20-10       MASS_7.3-22           multtest_2.14.0      
[16] parallel_2.15.2       pixmap_0.4-11         preprocessCore_1.20.0
[19] RColorBrewer_1.0-5    RCurl_1.95-4.1        RSQLite_0.11.4       
[22] splines_2.15.2        stats4_2.15.2         strucchange_1.4-7    
[25] survival_2.36-14      tilingArray_1.36.0    vsn_3.26.0           
[28] XML_3.98-1.1          xtable_1.7-1          zlibbioc_1.4.0       

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