Hi everybody, I'm trying to plot the exon probeset values for a gene, but alternative transcripts from Ensembl, or what GenomeGraphs calls "AffyModel" in the legend do not show up. Everything is the same as in the GenomeGraphs manual (and this is the problem!). Here is everything, including the txt files I used: require(GenomeGraphs) title <- makeTitle(text = "ENSG00000172716", color = "darkred") exon <- makeExonArray(intensity = undata, probeStart = unposition[, 3], probeEnd = unposition[,4], probeId = as.character(unposition[,1]), nProbes = unprobes, dp = DisplayPars(color = "blue", mapColor = "dodgerblue2"), displayProbesets = FALSE) affyModel.model <- makeGeneModel(start = unposition[,3], end = unposition[, 4]) # note that if you use this in the gdplot function, you will have a green gene, whereas with affyModel you get a blue gene affyModel <- makeAnnotationTrack(start = unposition[,3], end = unposition[, 4], feature = "gene_model", group = "ENSG00000172716", dp = DisplayPars(gene_model = "darkblue")) #adding this in gdplot returns a blue gene gene <- makeGene(id = "ENSG00000172716", biomart = mart) #no sign of this even after calling it in gdplot, and the legend shows that something yellow should appear transcript <- makeTranscript(id = "ENSG00000172716", type = "ensembl_gene_id", biomart = mart) #I suppose from other examples in GenomeGraphs that this should show the splice variants in Ensembl below the Affy model, but nothing appears legend <- makeLegend(c("affyModel", "gene"), fill = c("darkgreen", "orange")) rOverlay <- makeRectangleOverlay(start = 30701442, end = 30724798, region = c(3, 5), dp = DisplayPars(alpha = 0.2, fill = "olivedrab1")) gdPlot(list(title, exon, affyModel, gene, transcript, legend), minBase = 30701442, maxBase = 30724798,overlay = rOverlay) #note that since I don't want to overlay anything, I just used it as a box to encase the whole gene > sessionInfo() R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] GenomeGraphs_1.6.0 biomaRt_2.2.0 aroma.affymetrix_1.5.0 aroma.apd_0.1.7 [5] affxparser_1.18.0 R.huge_0.2.0 aroma.core_1.5.0 aroma.light_1.16.0 [9] matrixStats_0.2.1 R.rsp_0.3.6 R.cache_0.3.0 R.filesets_0.8.1 [13] digest_0.4.2 R.utils_1.4.0 R.oo_1.7.2 R.methodsS3_1.2.0 loaded via a namespace (and not attached): [1] RCurl_1.3-1 tools_2.10.1 XML_2.8-1 Thank you all! Gabriele Zoppoli, MD Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy Guest Researcher, LMP, NCI, NIH, Bethesda MD Work: 301-451-8575 Mobile: 301-204-5642 Email: zoppolig at mail.nih.gov -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: undata.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20100515="" dea170dd="" attachment.txt=""> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: unposition.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20100515="" dea170dd="" attachment-0001.txt=""> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: unprobes.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20100515="" dea170dd="" attachment-0002.txt="">