On Sep 10, 2008, at 12:25 PM, McGee, Monnie wrote: > Dear Robert, > > I am using R 2.7.2 with marray 1.18 (and BioC 1.18). I ran > Sys.locale and found the following: > >> Sys.getlocale() > [1] "en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8" > Then I set the Sys.locale to "C", as suggested. >> Sys.setlocale(locale = "C") > [1] "C/C/C/C/C/en_US.UTF-8" > > This solved the problem with the read.GenePix function. However, > the problem with the graphics device still remains. Here is the > code and the errors I received: > >> library(beta7) >> maQualityPlots(beta7) > Error in X11(paste("png::", filename, sep = ""), width, height, > pointsize, : > unable to start device PNG > In addition: Warning message: > In png(filename = "diagPlot.6Hs.195.1.png", width = 1600, height = > 1200, : > unable to open connection to X11 display '' > >> maQualityPlots(beta7,dev="jpeg") > Error in X11(paste("jpeg::", quality, ":", filename, sep = ""), > width, : > unable to start device JPEG > In addition: Warning message: > In jpeg(filename = "diagPlot.6Hs.195.1.jpeg", width = 1600, height = > 1200, : > unable to open connection to X11 display '' > >> maQualityPlots(beta7,dev="ps") > [1] "Format error, format will be set to PNG" > Error in X11(paste("png::", filename, sep = ""), width, height, > pointsize, : > unable to start device PNG > In addition: Warning message: > In png(filename = "diagPlot.6Hs.195.1.png", width = 1600, height = > 1200, : > unable to open connection to X11 display '' > > This happened while I was using R.app GUI 1.25 (5217). When I > opened an X11 window on my computer and tried the same code, it > worked. For some reason, R.app cannot open .png. .jpeg. or .ps. Is > there a fix for this? > Click on the X11 icon inside R.app, that will start X11. You need to have X11 running to do jpeg or png (although that has recently changed in a way to has not been incorporated into maQualityPlots. Kasper > Thanks, > Monnie > > Monnie McGee, Ph.D. > Associate Professor > Department of Statistical Science > Southern Methodist University > Ph: 214-768-2462 > Fax: 214-768-4035 > > > > -----Original Message----- > From: Robert Gentleman [mailto:rgentlem at fhcrc.org] > Sent: Tue 9/9/2008 5:34 PM > To: McGee, Monnie > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Problem following monograph directions in > Chapter 4 > > Hi Monnie, > > What you did not tell us is your sessionInfo(), so we don't know what > version of R/BioC you are using. If it is not 2.7.2 and 1.18.0 for > marray then you should update, and then ask. > > the other issue is that you have your locale set to something other > than > C (and sometimes it is just easier to set it to C) > > you can find out by looking at > Sys.getlocale > and set using Sys.setlocale > > and then those errors would most likely go away > > best wishes > Robert > > > McGee, Monnie wrote: >> Hello, All, >> >> First of all, I'm using R 2.7.2 with the latest version of BioC (I >> just downloaded everything last Friday). My machine is a 4 by >> 2.5 GHz PowerPC G5 running Mac OS 10.4.11. >> >> I am following the code in the monograph (and on the monograph >> website) to work through Chapter 4 of the monograph: Preprocessing >> Two-Color Arrays. I realize that R has gone through several >> versions since the text was printed. I think that my problems stem >> from using outdated code. >> >> My first question is about the error in the line "mraw = >> read.GenePix(files,name.Gb=NULL,name.Rb=NULL)". It says that >> "input string 32 is invalid". My second question is about the >> error when using maQualityPlots (last line of code below). >> >> >> The following is the code I typed and the output: >>> datadir = system.file("beta7",package="beta7") >>> TargetInfo = read.marrayInfo(file.path(datadir,"TargetBeta7.txt")) >>> TargetInfo at maNotes = "Files were loaded from beta7 package." >>> TargetInfo >> An object of class "marrayInfo" >> @maLabels >> [1] "6Hs.195.1.gpr" "6Hs.168.gpr" "6Hs.166.gpr" >> [4] "6Hs.187.1.gpr" "6Hs.194.gpr" "6Hs.243.1.gpr" >> >> @maInfo >> FileNames SubjectID Cy3 Cy5 Date of Blood Draw >> 1 6Hs.195.1.gpr 1 b7 - b7 + 2002.10.11 >> 2 6Hs.168.gpr 3 b7 + b7 - 2003.01.16 >> 3 6Hs.166.gpr 4 b7 + b7 - 2003.01.16 >> 4 6Hs.187.1.gpr 6 b7 - b7 + 2002.09.16 >> 5 6Hs.194.gpr 8 b7 - b7 + 2002.09.18 >> 6 6Hs.243.1.gpr 11 b7 + b7 - 2003.01.13 >> Date of Scan >> 1 2003.07.25 >> 2 2003.08.07 >> 3 2003.08.07 >> 4 2003.07.18 >> 5 2003.07.25 >> 6 2003.08.06 >> >> @maNotes >> [1] "Files were loaded from beta7 package." >> >>> galinfo = read.Galfile("6Hs.166.gpr",path=datadir) >> Error in if (skip > 0) readLines(file, skip) : >> missing value where TRUE/FALSE needed >> In addition: Warning messages: >> 1: In greplayout.id[1], y) : input string 32 is invalid in this >> locale >> 2: In grepinfo.id[1], y) : input string 32 is invalid in this locale >>> oldwd = getwd() >>> setwd(datadir) >>> files = c("6Hs.166.gpr","6Hs.187.1.gpr") >>> mraw = read.GenePix(files,name.Gb=NULL,name.Rb=NULL) >> Error in if (skip > 0) readLines(file, skip) : >> missing value where TRUE/FALSE needed >> In addition: Warning messages: >> 1: In greplayout.id[1], y) : input string 32 is invalid in this >> locale >> 2: In grepinfo.id[1], y) : input string 32 is invalid in this locale >>> library("beta7") >>> checkTargetInfo(beta7) >> [1] TRUE >>> maGeneTable(beta7)[1:4,1:5] >> Grid.R Grid.C Spot.R Spot.C ID >> H200000297 1 1 1 1 H200000297 >> H200000303 1 1 1 2 H200000303 >> H200000321 1 1 1 3 H200000321 >> H200000327 1 1 1 4 H200000327 >>> beta7nbg = beta7 >>> beta7nbg at maGb = beta7nbg at maRb = 0 * beta7nbg at maRb >>> beta7sub = beta7[1:100,2:3] >>> maQualityPlots(beta7) >> Error in X11(paste("png::", filename, sep = ""), width, height, >> pointsize, : >> unable to start device PNG >> In addition: Warning message: >> In png(filename = "diagPlot.6Hs.195.1.png", width = 1600, height = >> 1200, : >> unable to open connection to X11 display '' >> >> I also tried the following section of code from page 67 of the >> monograph with the same results: >> >>> library(arrayQuality) >>> TargetInfo = read.marrayInfo("TargetBeta7.txt") >>> mraw = read.GenePix(targets = TargetInfo) >> Error in if (skip > 0) readLines(file, skip) : >> missing value where TRUE/FALSE needed >> In addition: Warning messages: >> 1: In greplayout.id[1], y) : input string 32 is invalid in this >> locale >> 2: In grepinfo.id[1], y) : input string 32 is invalid in this locale >>> maQualityPlots(mraw) >> Error in as.vector(x) : object "mraw" not found >>> TargetInfo >> An object of class "marrayInfo" >> @maLabels >> [1] "6Hs.195.1.gpr" "6Hs.168.gpr" "6Hs.166.gpr" >> [4] "6Hs.187.1.gpr" "6Hs.194.gpr" "6Hs.243.1.gpr" >> >> @maInfo >> FileNames SubjectID Cy3 Cy5 Date of Blood Draw >> 1 6Hs.195.1.gpr 1 b7 - b7 + 2002.10.11 >> 2 6Hs.168.gpr 3 b7 + b7 - 2003.01.16 >> 3 6Hs.166.gpr 4 b7 + b7 - 2003.01.16 >> 4 6Hs.187.1.gpr 6 b7 - b7 + 2002.09.16 >> 5 6Hs.194.gpr 8 b7 - b7 + 2002.09.18 >> 6 6Hs.243.1.gpr 11 b7 + b7 - 2003.01.13 >> Date of Scan >> 1 2003.07.25 >> 2 2003.08.07 >> 3 2003.08.07 >> 4 2003.07.18 >> 5 2003.07.25 >> 6 2003.08.06 >> >> @maNotes >> [1] "TargetBeta7.txt" >> >> >> Thanks for your help! >> >> Monnie McGee, Ph.D. >> Associate Professor >> Department of Statistical Science >> Southern Methodist University >> Ph: 214-768-2462 >> Fax: 214-768-4035 >> >> >> >> >> >> ------------------------------------------------------------------- ----- >> >> _______________________________________________ >> 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 > > -- > Robert Gentleman, PhD > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > PO Box 19024 > Seattle, Washington 98109-1024 > 206-667-7700 > rgentlem at fhcrc.org > > _______________________________________________ > 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