[BioC] question about QCReport

[Saroj Mohapatra]

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/11810/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
> ------------------------------------------------------------------------
>
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