[BioC] gpQuality and readGPR errors for Microarrays [arrayQuality Package]

[Edra [guest]]

Hi all,

I am running a few quality checks on my microarray data (GenePix). I receive this error when trying to run the gpQuality() function from the "arrayQuality" package for my GenePix microarrays (.gpr files). I investigated further and noticed error messages for the readGPR function as well. I performed the readGPRheader function, which identified 31 headers in my file, but I actually have 48. Should I set up my own reference slide quality control measures for the gpQuality function or is it more of an internal error (OS compatibility or bug in package)?

Thanks for any help and advice!

Edra S.
Graduate Student
M.S Medical Biology
Long Island University


> 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")
> warnings()
Warning messages:
1: In strsplit(readLines(f, n = skip + 1), split = sep) :
  input string 6 is invalid in this locale
2: In strsplit(readLines(f, n = skip + 1), split = sep) :
  input string 9 is invalid in this locale
3: In strsplit(readLines(f, n = skip + 1), split = sep) :
  input string 32 is invalid in this locale
4: In min(x) : no non-missing arguments to min; returning Inf
5: In max(x) : no non-missing arguments to max; returning -Inf
6: In min(x) : no non-missing arguments to min; returning Inf
7: In max(x) : no non-missing arguments to max; returning -Inf
8: In min(x) : no non-missing arguments to min; returning Inf
9: In max(x) : no non-missing arguments to max; returning -Inf
10: In min(x) : no non-missing arguments to min; returning Inf
11: In max(x) : no non-missing arguments to max; returning -Inf

readGPR function on one of my gpr files (same error message for all files):

 gprData <- readGPR(fnames="H003-3100512996.gpr", path=datadir)
Warning messages:
1: In strsplit(readLines(f, n = skip + 1), split = sep) :
  input string 6 is invalid in this locale
2: In strsplit(readLines(f, n = skip + 1), split = sep) :
  input string 9 is invalid in this locale
3: In strsplit(readLines(f, n = skip + 1), split = sep) :
  input string 32 is invalid in this locale


Other relevant info:

*Running on OS X Mavericks

*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.


 -- 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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