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 -- Sent via the guest posting facility at bioconductor.org.