Dear Agnes,
I saw in the internet that you helped someone with some R bugs, so I was wondering if you could help me as well.  Any help will be more than welcome.
I am trying to use arrayQuality program in R, but I couldn't make it work with my slides. I'm not working with human genome or mouse. I'm working with another organism, so I am trying to customize my gpQuality.
I have 2 questions:
 In the pg 24 of the arrayQualitymanual ( http://ugrad.ubc.ca/R/library/arrayQuality/doc/guide.html) (fig8). After I generate the myspottypes.txt file, I cannot make it pass the column name as argument with the command.
> controlCode <- readcontrolCode(file="myspottype.txt", controlID="ID")
Do I need to do something else with the file first before using this command after I save the file as txt file? Also if I just use my controlcode file I get some errors. I copied everything that I have done to run the program and the errrors that I get. BTW, I am using genepix, so my files are GPR files.
 Can you help me with the errors that I get at the end. Am I doing something wrong?
I really appreciate your help.
Thank you.
Debora

> library(arrayQuality)
Loading required package: marray
Loading required package: limma
Loading required package: limma
Loading required package: convert
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: hexbin
Loading required package: grid
Loading required package: lattice
Loading required package: colorspace

Attaching package: 'colorspace'


        The following object(s) are masked from package:grDevices :

         hcl 

Loading required package: gridBase
Loading required package: RColorBrewer
Warning messages:
1: package 'limma' was built under R version 2.3.1 
2: package 'Biobase' was built under R version 2.3.1 
> read.table("controls.txt")
       V1                  V2
1 Pattern                Name
2   exig*              Probes
3   blank               blank
4      H*       Human_control
5      A* Arabidopsis_control
6   gDNA*       Exiguo_genome
7 G_exig*        Group_probes
> controlcode <- read.table("controls.txt", header=TRUE, sep="\t")
> controlcode
  Pattern                Name
1   exig*              Probes
2   blank               blank
3      H*       Human_control
4      A* Arabidopsis_control
5   gDNA*       Exiguo_genome
6 G_exig*        Group_probes
> controlcode <- as.matrix(controlcode)
> class(controlcode)
[1] "matrix"
> controlcode
  Pattern   Name                 
1 "exig*"   "Probes"             
2 "blank"   "blank"              
3 "H*"      "Human_control"      
4 "A*"      "Arabidopsis_control"
5 "gDNA*"   "Exiguo_genome"      
6 "G_exig*" "Group_probes"       
> globalQuality(fnames=NULL, path=".", organism="Exiguobacterium")
Error in var(log.na(gprData[["GbMedian"]], 2), na.rm = TRUE) : 
        'x' is empty
In addition: Warning messages:
1: no non-missing arguments to min; returning Inf 
2: no non-missing arguments to max; returning -Inf 
3: no non-missing arguments to min; returning Inf 
4: no non-missing arguments to max; returning -Inf 
> gpQuality (organism="Exiguobacterium", reference=NULL, controlMatrix=controlcode, controlID="ID")
[1] "Starting gpQuality..."
Error in var(log.na(gprData[["GbMedian"]], 2), na.rm = TRUE) : 
        'x' is empty
In addition: Warning messages:
1: no non-missing arguments to min; returning Inf 
2: no non-missing arguments to max; returning -Inf 
3: no non-missing arguments to min; returning Inf 
4: no non-missing arguments to max; returning -Inf 

Debora Frigi Rodrigues
rodri257@msu.edu
Graduate Assistant
Microbiology and Molecular Genetics
Center for Microbial Ecology
Plant and Soil Science Room 540
Michigan State University
East Lansing, MI 48824
Phone: 517-355-0271 ext 284 
Fax: 517-353-2917
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