[BioC] gpQuality Error

Edra [guest] guest at bioconductor.org
Fri Aug 8 03:11:12 CEST 2014


Hi all,

I get this error when trying to run the gpQuality() function from the "arrayQuality" package for my GenePix microarrays (.gpr files).

> gpQuality()
[1] "Starting gpQuality..."
Error in if (abs(MMR[i]) > 0.5) numSpotOverMmrLim <- numSpotOverMmrLim +  : 
  missing value where TRUE/FALSE needed
In addition: There were 11 warnings (use warnings() to see them)
> gpQuality(organism = "Hs")
[1] "Starting gpQuality..."
Error in if (abs(MMR[i]) > 0.5) numSpotOverMmrLim <- numSpotOverMmrLim +  : 
  missing value where TRUE/FALSE needed
In addition: There were 11 warnings (use warnings() to see them)
> traceback()
2: slideQuality(gp, controlMatrix = controlMatrix, DEBUG = DEBUG)
1: gpQuality(organism = "Hs")


I changed my locale to as seen below because of error messages when running the read.GenePix function.

maQualityPlots() works fine. There was a minor error initially:

maQualityPlots(data.raw)
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'

5: xy.coords(x, y, xlabel, ylabel, log)
4: plot.default(bin, xlab = "A", ylab = "M", main = main, colramp = col, 
       colorcut = colorcut, maxcnt = maxcnt, legend = 1, lcex = 1, 
       newpage = FALSE)
3: plot(bin, xlab = "A", ylab = "M", main = main, colramp = col, 
       colorcut = colorcut, maxcnt = maxcnt, legend = 1, lcex = 1, 
       newpage = FALSE)
2: qpHexbin(mnorm, main = "MA-Plot :: Norm")
1: maQualityPlots(data.raw)

But then I used the trace function to edit the qpHexbin function to plot using gplot.hexbin instead of the internal plot function.

Thanks for any help and advice!

Edra

 -- output of sessionInfo(): 

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] en_US/en_US/en_US/C/en_US/en_US.UTF-8

attached base packages:
[1] grid      parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] hexbin_1.26.3       lattice_0.20-29     arrayQuality_1.42.0
[4] vsn_3.32.0          convert_1.40.0      Biobase_2.24.0     
[7] BiocGenerics_0.10.0 marray_1.42.0       limma_3.20.8       

loaded via a namespace (and not attached):
[1] affy_1.42.3           affyio_1.32.0         BiocInstaller_1.14.2 
[4] gridBase_0.4-7        preprocessCore_1.26.1 RColorBrewer_1.0-5   
[7] zlibbioc_1.10.0      
> 

--
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