Dear all, I want to use cPlot and cColor from the geneplotter package to visualise the intensity level of some genes from a microarray experiment on their given chromosomal location. However, I'm slightly confused by the results, especially since the colours don't really match what I get using alongChrom(). An example is shown below, using Entrez IDs. In this case I would expect the first probe in the "probes" argument to be associated with the first colour in "color" and so on, but that doesn't seem to be the case. At least not for my versions of the packages. Any comments would be appreciated. Also, out of curiosity, what happens with those IDs that map to several locations within the genome, such as no. 19 and 64 in my xx list. Will the "color" argument automatically take that into consideration? Thanks \Heidi library(geneplotter) library(org.Mm.eg.db) library(RColorBrewer) # Test x <- org.Mm.egCHRLOC mapped_genes <- mappedkeys(x) xx <- as.list(x[mapped_genes]) chr <- buildChromLocation("org.Mm.eg.db") cPlot(chr) cColor(probes=names(xx[1:4]), color=c("red", "green", "blue", "purple"), plotChroms=chr) # A (simplified) example similar to the vignette dec <- quantile(0:100, probs=seq(0,1,0.1)) class <- cut(1:100, dec) col <- brewer.pal(10, "RdYlGn") cPlot(chr) cColor(probes=names(xx[1:100]), color=col[class], plotChroms=chr) sessionInfo() R version 2.7.0 Patched (2008-05-18 r45723) i386-apple-darwin8.10.1 locale: en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] RColorBrewer_1.0-2 org.Mm.eg.db_2.2.0 geneplotter_1.18.0 annotate_1.18.0 xtable_1.5-2 [6] AnnotationDbi_1.2.0 RSQLite_0.6-8 DBI_0.2-4 lattice_0.17-7 Biobase_2.0.1 loaded via a namespace (and not attached): [1] KernSmooth_2.22-22 grid_2.7.0