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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:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=de_BE.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=de_BE.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=de_BE.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=de_BE.UTF-8 LC_IDENTIFICATION=C attached base packages:  parallel stats graphics grDevices utils datasets methods  base other attached packages:  copynumber_1.1.1 BiocGenerics_0.6.0 loaded via a namespace (and not attached):  GenomicRanges_1.12.5 IRanges_1.18.4 stats4_3.0.2  tools_3.0.2 -- Sent via the guest posting facility at bioconductor.org.