[BioC] Problem following monograph directions in Chapter 4
McGee, Monnie
mmcgee at mail.smu.edu
Wed Sep 10 21:25:15 CEST 2008
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?
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 grep(layout.id[1], y) : input string 32 is invalid in this locale
> 2: In grep(info.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 grep(layout.id[1], y) : input string 32 is invalid in this locale
> 2: In grep(info.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 grep(layout.id[1], y) : input string 32 is invalid in this locale
> 2: In grep(info.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
>
>
>
>
>
> ------------------------------------------------------------------------
>
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--
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
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