hi, ive proccessed chromosomeExplorer for all the chromosomes and i get many plots but also the error (although it doesnt stop cause of it)... if i do the traceback i get this
>traceback() 32: unlist(args) 31: as.list(unlist(args)) 30: par("lwd") 29: int_abline(a = a, b = b, h = h, v = v, untf = untf, ...) 28: abline(h = log2(level), col = "blue", lty = 2) 27: withCallingHandlers(expr, warning = function(w) invokeRestart ("muffleWarning")) 26: suppressWarnings({ newPlot(this, xlim = xlim, ylim = ylim, flavor = "ce", unit = unit, ...) drawXAxisRuler(xrange = c(0, nbrOfBases)/10^unit, ticksBy = ticksBy) if (!identical(this$.plotCytoband, FALSE)) { drawCytoband(this, chromosome = chromosome, unit = unit) } cnLevels <- c(1/2, 1, 3/2) for (level in cnLevels) { abline(h = log2(level), col = "blue", lty = 2) } rawCns <- extractRawCopyNumbers(fit) verbose && print(verbose, rawCns, level = -50) n <- nbrOfLoci(rawCns, na.rm = TRUE) stext(text = sprintf("n=%d", n), side = 4, pos = 0, line = 0, cex = 0.8) pointsRawCNs(fit, unit = unit, ...) cnRegions <- extractCopyNumberRegions(fit) verbose && print(verbose, cnRegions, level = -50) drawLevels(cnRegions, lwd = 4, col = "black", xScale = 1/10^unit) drawExtraAnnotations(fit) onFitAddGenotypeCalls(fit, callList = callList, arrayName = arrayName, resScale = 10^unit * resScale, ...) }) 25: doTryCatch(return(expr), name, parentenv, handler) 24: tryCatchOne(expr, names, parentenv, handlers[[1]]) 23: tryCatchList(expr, classes, parentenv, handlers) 22: tryCatch({ verbose && enter(verbose, "Plotting graph") opar <- par(xaxs = "r") suppressWarnings({ newPlot(this, xlim = xlim, ylim = ylim, flavor = "ce", unit = unit, ...) drawXAxisRuler(xrange = c(0, nbrOfBases)/10^unit, ticksBy = ticksBy) if (!identical(this$.plotCytoband, FALSE)) { drawCytoband(this, chromosome = chromosome, unit = unit) } cnLevels <- c(1/2, 1, 3/2) for (level in cnLevels) { abline(h = log2(level), col = "blue", lty = 2) } rawCns <- extractRawCopyNumbers(fit) verbose && print(verbose, rawCns, level = -50) n <- nbrOfLoci(rawCns, na.rm = TRUE) stext(text = sprintf("n=%d", n), side = 4, pos = 0, line = 0, cex = 0.8) pointsRawCNs(fit, unit = unit, ...) cnRegions <- extractCopyNumberRegions(fit) verbose && print(verbose, cnRegions, level = -50) drawLevels(cnRegions, lwd = 4, col = "black", xScale = 1/10^unit) drawExtraAnnotations(fit) onFitAddGenotypeCalls(fit, callList = callList, arrayName = arrayName, resScale = 10^unit * resScale, ...) }) stext(chipType, side = 4, pos = 1, line = 0, cex = 0.8) verbose && exit(verbose) }, error = function(ex) { print(ex) }, finally = { par(opar) if (!imageFormat %in% c("screen", "current")) dev.off() }) 21: doTryCatch(return(expr), name, parentenv, handler) 20: tryCatchOne(expr, names, parentenv, handlers[[1]]) 19: tryCatchList(expr, classes, parentenv, handlers) 18: tryCatch({ arrayFullName <- gsub("^(.*),chr[0-9][0-9].*$", "\\1", fullname) arrayName <- gsub("^([^,]*).*$", "\\1", arrayFullName) nbrOfBases <- genome$nbrOfBases[chromosome] widthMb <- nbrOfBases/10^unit if (is.null(xlim)) { xlim <- c(0, getChromosomeLength(chromosome))/10^unit } verbose && enter(verbose, sprintf("Plotting %s for chromosome %02d [%.2fMB]", arrayName, chromosome, widthMb)) for (zz in seq(along = zooms)) { zoom <- zooms[zz] imgName <- sprintf("%s,chr%02d,x%04d.%s", arrayFullName, chromosome, zoom, imageFormat) pathname <- filePath(path, imgName) pathname <- gsub(" ", "_", pathname) if (!imageFormat %in% c("screen", "current")) { if (skip && isFile(pathname)) { next } } ticksBy <- 10^ceiling(log10(pixelsPerTick/(zoom * pixelsPerMb))) width <- round(zoom * widthMb * pixelsPerMb + sum (xmargin)) verbose && printf(verbose, "Pathname: %s\n", pathname) verbose && printf(verbose, "Dimensions: %dx%d\n", width, height) verbose && printf(verbose, "Ticks by: %f\n", ticksBy) if (!is.null(plotDev)) plotDev(pathname, width = width, height = height) tryCatch({ verbose && enter(verbose, "Plotting graph") opar <- par(xaxs = "r") suppressWarnings({ newPlot(this, xlim = xlim, ylim = ylim, flavor = "ce", unit = unit, ...) drawXAxisRuler(xrange = c(0, nbrOfBases)/10^unit, ticksBy = ticksBy) if (!identical(this$.plotCytoband, FALSE)) { drawCytoband(this, chromosome = chromosome, unit = unit) } cnLevels <- c(1/2, 1, 3/2) for (level in cnLevels) { abline(h = log2(level), col = "blue", lty = 2) } rawCns <- extractRawCopyNumbers(fit) verbose && print(verbose, rawCns, level = -50) n <- nbrOfLoci(rawCns, na.rm = TRUE) stext(text = sprintf("n=%d", n), side = 4, pos = 0, line = 0, cex = 0.8) pointsRawCNs(fit, unit = unit, ...) cnRegions <- extractCopyNumberRegions(fit) verbose && print(verbose, cnRegions, level = -50) drawLevels(cnRegions, lwd = 4, col = "black", xScale = 1/10^unit) drawExtraAnnotations(fit) onFitAddGenotypeCalls(fit, callList = callList, arrayName = arrayName, resScale = 10^unit * resScale, ...) }) stext(chipType, side = 4, pos = 1, line = 0, cex = 0.8) verbose && exit(verbose) }, error = function(ex) { print(ex) }, finally = { par(opar) if (!imageFormat %in% c("screen", "current")) dev.off() }) } }, error = function(ex) { cat("ERROR caught in ", hookName, "():\n", sep = "") print(ex) }, finally = { gc <- gc() verbose && print(verbose, gc) verbose && exit(verbose) }) 17: fcn(...) 16: doTryCatch(return(expr), name, parentenv, handler) 15: tryCatchOne(expr, names, parentenv, handlers[[1]]) 14: tryCatchList(expr, classes, parentenv, handlers) 13: tryCatch({ result <- fcn(...) tmp[["result"]] <- result failedHooks[kk] <- FALSE }, error = function(ex) { tmp[["exception"]] <<- ex }) 12: callHooks.list(hooks, ...) 11: callHooks(hooks, ...) 10: callHooks.default(hookName, fit = fit, chromosome = chr, fullname = fullname) 9: callHooks(hookName, fit = fit, chromosome = chr, fullname = fullname) 8: fit.CopyNumberSegmentationModel(this, ..., .retResults = FALSE, verbose = verbose) 7: fit(this, ..., .retResults = FALSE, verbose = verbose) 6: plot.CopyNumberSegmentationModel(model, path = path, imageFormat = "png", plotband = plotband, arrays = arrays, ...) 5: plot(model, path = path, imageFormat = "png", plotband = plotband, arrays = arrays, ...) 4: writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes = chromosomes, ..., verbose = less(verbose)) 3: writeGraphs(this, arrays = arrays, chromosomes = chromosomes, ..., verbose = less(verbose)) 2: process.ChromosomeExplorer(ce, verbose = verbose) 1: process(ce, verbose = verbose) ive also tried with the R v2.8.0patched and it gives the same error... thanks, marĂa --~--~---------~--~----~------------~-------~--~----~ When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. 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