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Question: GenePlotter - new user question
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15.0 years ago by
Chris Doucette10 wrote:
Hi, I've just recently started using the bioconductor packages. I'm trying to set up the example script for "Whole Genome Plotting" in the help file called visualize.pdf (I'll paste it in at the end of the message). When the script runs in R, I notice three differences between the image that's generated and the sample image in the PDF: 1) The lengths of the chromosomes are nearly uniform, whereas they vary greatly in the PDF (the Y chromosome is almost as long as chromosome 1!) 2) Only 8 or so genes are colored in by cColor, whereas there are a few hundred colored genes in the PDF 3) The script generates "50 or more" (apparently 50 is the limit) warnings which all say the same thing: the condition has length > 1 and only the first element will be used in: if is.na(y)) y else names(y) I'm somewhat unfamiliar with R and I'm entirely in the dark as to what's causing the problem. One person suggested that the data package (hgu95av2) might have corrupted data. I've tried other packages from the website and the same thing happens. I have been able to track the source of the warnings to the call to chrObj <- buildChromLocation("hgu95av2"). I'm still not sure what it means or what effect it's having on the results. Here's the script I'm trying to run (copied verbatim from the PDF): library(geneplotter) data(eset) mytt <- function(y) { ys <- split(y, cov2) t.test(ys[[1]], ys[[2]]) } ttout <- esApply(eset, 1, mytt) s1means <- sapply(ttout, function(x) x$estimate[1]) s2means <- sapply(ttout, function(x) x$estimate[2]) deciles <- quantile(c(s1means, s2means), probs = seq(0, 1, 0.1)) s1class <- cut(s1means, deciles) names(s1class) <- names(s1means) s2class <- cut(s2means, deciles) names(s2class) <- names(s2means) cols <- dChip.colors(10) nf <- layout(matrix(1:3,nr=1), widths=c(5,5,2)) chrObj <- buildChromLocation("hgu95av2") cPlot(chrObj) cColor(geneNames(eset), cols[s1class], chrObj) cPlot(chrObj) cColor(geneNames(eset), cols[s2class], chrObj) image(1,1:10,matrix(1:10,nc=10),col=cols, axes=FALSE, xlab="", ylab="") axis(2, at=(1:10), labels=levels(s1class), las=1) Has anyone experienced a similar issue trying to run this script? Is there an updated version of the packages I should download? (I ran the installation yesterday using "Install from Bioconductor site" so theoretically the latest versions should all be there...) Thanks, - Chris Doucette doucett@fas.harvard.edu