Hello, I'm new to R and Bioconductor, and I was going through the tutorial in the "Quick start guide for marray". When I entered the line "> maQualityPlots(mraw)", I got this error message: "Error in baseViewports() : could not find function "viewport". My code follows the tutorial, exactly, which is: > library(marray) Loading required package: limma > dir(system.file("swirldata", package = "marray")) [1] "fish.gal" "swirl.1.spot" "swirl.2.spot" "swirl.3.spot" [5] "swirl.4.spot" "SwirlSample.txt" > datadir <- system.file("swirldata", package = "marray") > swirlTargets <- read.marrayInfo(file.path(datadir, "SwirlSample.txt")) > mraw <- read.Spot(targets = swirlTargets, path = datadir) Reading ... C:/PROGRA~1/R/R-211~1.0/library/marray/swirldata/swirl.1.spot Reading ... C:/PROGRA~1/R/R-211~1.0/library/marray/swirldata/swirl.2.spot Reading ... C:/PROGRA~1/R/R-211~1.0/library/marray/swirldata/swirl.3.spot Reading ... C:/PROGRA~1/R/R-211~1.0/library/marray/swirldata/swirl.4.spot > galinfo <- read.Galfile("fish.gal", path = datadir) > mraw at maLayout <- galinfo$layout > mraw at maGnames <- galinfo$gnames > library(arrayQuality) > maQualityPlots(mraw) Error in baseViewports() : could not find function "viewport" I am running R 2.11.0, and Bioconductor 2.6. Please let me know If I need to provide any more information. Greatly appreciated, Jason Zoller UT MD Anderson Cancer Center Experimental Therapeutics Research Assistant 2

Hi Jason, First off, you should always cc the package maintainer in case she doesn't subscribe to the list, or on the off-chance she misses this email (cc'ed now). Zoller,Jason R wrote: > Hello, > > I'm new to R and Bioconductor, and I was going through the tutorial in the "Quick start guide for marray". When I entered the line "> maQualityPlots(mraw)", I got this error message: "Error in baseViewports() : could not find function "viewport". My code follows the tutorial, exactly, which is: > >> library(marray) > Loading required package: limma >> dir(system.file("swirldata", package = "marray")) > [1] "fish.gal" "swirl.1.spot" "swirl.2.spot" "swirl.3.spot" > [5] "swirl.4.spot" "SwirlSample.txt" >> datadir <- system.file("swirldata", package = "marray") >> swirlTargets <- read.marrayInfo(file.path(datadir, "SwirlSample.txt")) >> mraw <- read.Spot(targets = swirlTargets, path = datadir) > Reading ... C:/PROGRA~1/R/R-211~1.0/library/marray/swirldata/swirl.1.spot > Reading ... C:/PROGRA~1/R/R-211~1.0/library/marray/swirldata/swirl.2.spot > Reading ... C:/PROGRA~1/R/R-211~1.0/library/marray/swirldata/swirl.3.spot > Reading ... C:/PROGRA~1/R/R-211~1.0/library/marray/swirldata/swirl.4.spot >> galinfo <- read.Galfile("fish.gal", path = datadir) >> mraw at maLayout <- galinfo$layout >> mraw at maGnames <- galinfo$gnames >> library(arrayQuality) >> maQualityPlots(mraw) > Error in baseViewports() : could not find function "viewport" I see two problems here. 1.) The viewport() function isn't being imported to arrayQuality. You can get around that by loading the gridBase package yourself. 2.) Somehow the dispatch on plot() is being messed up. If you load gridBase and then call maQualityPlots, you will get an error stating that Error in as.double(y) : cannot coerce type 'S4' to vector of type 'double' However, if you debug(arrayQuality:::qpHexbin), directly load the hexbin package, specifically initialize a plotting window using x11(), and then substitute gplot.hexbin(bin, xlab="A", ylab="M", main=main, colramp=col, colorcut=colorcut,maxcnt=maxcnt, legend=1, lcex=1, newpage=F) for plot(bin, xlab = "A", ylab = "M", main = main, colramp = col, colorcut = colorcut, maxcnt = maxcnt, legend = 1, lcex = 1, newpage = FALSE) then you will get the plot you are looking for. Best, Jim > > I am running R 2.11.0, and Bioconductor 2.6. Please let me know If I need to provide any more information. > > Greatly appreciated, > > Jason Zoller > UT MD Anderson Cancer Center > Experimental Therapeutics > Research Assistant 2 > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues