[BioC] Problem following monograph directions in Chapter 4

[McGee, Monnie]

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  I think that my problems stem from using outdated code.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