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) 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=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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 > -- Sent via the guest posting facility at bioconductor.org.