After I run QCReport, I got the following error message: Error in FUN(c("AFFX-Ptp-actin-3_s_at", "AFFX-Ptp-actin-5_s_at", "AFFX-Ptp-actin-M_s_at", : subscript out of bounds Error in plot(qc(object)) : error in evaluating the argument 'x' in selecting a method for function 'plot' After I run GCOS, I found that there are no "AFFX-Ptp-actin-5_s_at" in probesetID list. Any one knows how could I solve this problem? The chip I used is Affymetrix poplars chip. Best yan

Hi Yan: Although we talked offline, I am responding to your message here. It would be nice if you send the output of sessionInfo() and the code that can reproduce the error. Looking at the function QCReport > QCReport function (object, file = "AffyQCReport.pdf", ...) { pdf(file = file, width = 8, height = 11, onefile = TRUE) plot.window(c(1, 1), c(0, 1)) plot.new() titlePage(object) signalDist(object) plot(qc(object)) borderQC1(object) borderQC2(object) correlationPlot(object) dev.off() return(TRUE) } Your error comes from qc(object). If you can re-run the code without the line plot(qc(object)), you would get the other results. Another thing to note is that poplar annotation is not available at bioconductor. Looking at http://www.bioconductor.org/packages/release/data/annotation/, there is a poplarcdf and poplarprobe but not a poplar.db. This post on bioc mailing list in 2007 describes the difficulty in building a poplar annotation package. Perhaps the same problems apply even now. http://article.gmane.org/gmane.science.biology.informatics.conductor/1 1810/match=poplar Good luck. Saroj Yan Zhang wrote: > After I run QCReport, I got the following error message: > > Error in FUN(c("AFFX-Ptp-actin-3_s_at", "AFFX-Ptp-actin-5_s_at", > "AFFX-Ptp-actin-M_s_at", : > subscript out of bounds > Error in plot(qc(object)) : > error in evaluating the argument 'x' in selecting a method for > function 'plot' > > After I run GCOS, I found that there are no "AFFX-Ptp-actin-5_s_at" in > probesetID list. > Any one knows how could I solve this problem? > The chip I used is Affymetrix poplars chip. > > Best > yan > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor