Hi, I'm using the GenomeGraphs package to plot expression data for multiple sample groups, and I've run into something that may or may not be classed as a bug. I've been using DisplayPars(color=c('blue','red')) to visually differentiate between sample groups, and that works well under most circumstances. However, I've found that when using e.g. makeGenericArray() that the addition of a probeEnd argument renders the graph using only the first colour in the DisplayPars list. Example code and sessionInfo() attached below. I only noticed this because I happened to try using DisplayPars(type="line") with probeStart and probeEnd to indicate the length of the interrogated genome region on the plots. Aside from this minor niggle, nice package! Cheers, Tim Rayner ## Example code follows: testGenomePlot <- function () { require('GenomeGraphs') data("exampleData", package = "GenomeGraphs") minBase <- 180292097 maxBase <- 180492096 ## Replace the default intensity data for example's sake (we need two samples) intensity <- matrix(rnorm(184), ncol=2) expres <- makeGenericArray(intensity = intensity, probeStart = exonProbePos, dp = DisplayPars( color = c("blue","red"), type = "point", lwd=2)) expres2 <- makeGenericArray(intensity = intensity, probeStart = exonProbePos, probeEnd = exonProbePos+200, # different dp = DisplayPars( color = c("blue","red"), type = "point", lwd=2)) gdPlot(list(good=expres, bad=expres2), minBase = minBase, maxBase = maxBase) } testGenomePlot() sessionInfo() R version 2.8.1 Patched (2009-01-19 r47650) i386-apple-darwin9.6.0 locale: en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomeGraphs_1.2.3 biomaRt_1.16.0 loaded via a namespace (and not attached): [1] RCurl_0.94-1 XML_1.99-0 tools_2.8.1