Dear List, I have been successfully using library "GenomeGraphs" to draw a figure with affy's exon array intensity data and Ensemble geneAnnotaion track. My qustion is how can I replace the Ensembl transcript annotation track with UCSC knownGene track or NCBI's RefSeq track? Below is my code for Ensembl track library(GenomeGraphs) mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") title <- makeTitle(text = "Test") exon <- makeExonArray(intensity = arrayData) affyModel.model <- makeGeneModel(start = unrPositions$start, end = unrPositions$stop) affyModel <- makeAnnotationTrack(start = unrPositions$start, end = unrPositions$stop, feature = "gene_model",group = geneid[i], dp = DisplayPars(gene_model = "darkblue")) transcript<-new("Transcript",id=unique(gene@ens [,"ensembl_gene_id"]),biomart=mart,dp=DisplayPars(plotId=TRUE)) plusStrand <- makeGeneRegion(chromosome = as.character(unrPositions[1,"seqname"]),start = min(unrPositions$start), end = max(unrPositions$stop), strand = as.character(unrPositions[1,"strand"]), biomart = mart) gdPlot(list(title, exon, affyModel, ga, transcript, legend), minBase = min(unrPositions$start),maxBase = max(unrPositions$stop)) > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 [5] LC_MONETARY=C LC_MESSAGES=en_US.iso885915 [7] LC_PAPER=en_US.iso885915 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomeGraphs_1.8.0 biomaRt_2.4.0 loaded via a namespace (and not attached): [1] RCurl_1.4-3 XML_3.1-1 Many thanks, Shirley <zhangxl@bu.edu> <zhangxl@bu.edu> [[alternative HTML version deleted]]