This is somewhat related to this question, I just want some more clarification. https://stat.ethz.ch/pipermail/bioconductor/2007-September/019138.html This is probably a silly question. I want to use the CNA function, but what are the elements of the vector you pass to maploc supposed to contain. >From an agilent data set I have a SystematicName column with elements of the form chr3:175483690-175483690. So for example for this element the chromosome # is 3, so the vector of these #s for all elements is passed as chrom in the CNA function. Great, but what is the position numeric passed to maploc? Maplocs argument has to be numeric from the DNAcopy documentation so its one #. Is it the first value 175483690, 175483690 , or the average of the two? I cant seem to find any clarification on this anywhere. -- output of sessionInfo(): > sessionInfo() R version 3.1.1 (2014-07-10) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] snapCGH_1.34.0 DNAcopy_1.38.1 limma_3.20.8 loaded via a namespace (and not attached): [1] aCGH_1.42.0 affy_1.42.3 affyio_1.32.0 [4] annotate_1.42.1 AnnotationDbi_1.26.0 Biobase_2.24.0 [7] BiocGenerics_0.10.0 BiocInstaller_1.14.2 cluster_1.15.2 [10] DBI_0.2-7 genefilter_1.46.1 GenomeInfoDb_1.0.2 [13] GLAD_2.28.1 grid_3.1.1 IRanges_1.22.9 [16] lattice_0.20-29 MASS_7.3-33 multtest_2.20.0 [19] parallel_3.1.1 pixmap_0.4-11 preprocessCore_1.26.1 [22] RColorBrewer_1.0-5 RSQLite_0.11.4 sandwich_2.3-1 [25] splines_3.1.1 stats4_3.1.1 strucchange_1.5-0 [28] survival_2.37-7 tilingArray_1.42.0 tools_3.1.1 [31] vsn_3.32.0 XML_3.98-1.1 xtable_1.7-3 [34] zlibbioc_1.10.0 zoo_1.7-11 -- Sent via the guest posting facility at bioconductor.org.