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 > -- Sent via the guest posting facility at bioconductor.org.