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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:
[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
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