Question: CGHCall problems
gravatar for Guest User
3.8 years ago by
Guest User12k
Guest User12k wrote:
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
ADD COMMENTlink written 3.8 years ago by Guest User12k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 259 users visited in the last hour