[BioC] Problem with ABarray package

[Alison Ziesel]

Hello Conductors,

I have very recently started using R and BioConductor to help with  
array analysis for my supervisor and co-workers. I must confess that  
I am very much a beginner and I apologize in advance if the question  
posed is too basic for this list.

The first and only BioC package I've been using is ABarray. After  
getting R working and running the BiocLite.R install package for  
BioConductor, I then installed ABarray and its requisite packages. I  
run the basic analysis for ABarray but consistently run into an error  
as seen below:


 > Sys.putenv("R_GSCMD"="/usr/local/bin/gs")
 > library(ABarray)
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: multtest
Loading required package: survival
Loading required package: splines


Welcome to Applied Biosystems AB1700
      This package performs analysis for AB1700
      gene expression data
 > eset = ABarray("HFE1rawdata.txt", "hfe1_design.txt", "tissue")
Using assayName to match experiment with signal in file: HFE1rawdata.txt
The sample names are:
[1] "HFE-1" "HFE-2"
AssayNames in dataFile: HFE1rawdata.txt
[1] "HB00BA6_1/23/07_9:36_AM" "HB00BTX_1/23/07_9:51_AM"
Reading data from HFE1rawdata.txt ......
     This may take several minutes....
Checking data format:::::::||

The results will be in the folder: Result_tissue/
[1] "Creating plot for Signal Hybridization_Control ..."
[1] "Creating plot for Signal Negative_Control ..."
[1] "Creating plot for Signal IVT_Kit_Control_BIOB ..."
[1] "Creating plot for Signal IVT_Kit_Control_BIOC ..."
[1] "Creating plot for Signal IVT_Kit_Control_BIOD ..."
[1] "Creating plot for Signal RT_Kit_Control_DAP ..."
[1] "Creating plot for Signal RT_Kit_Control_LYS ..."
[1] "Creating plot for Signal RT_Kit_Control_PHE ..."

Perform basic analysis for non-normalized data ...
[1] "Creating barplot for probes detectable ... QC_DetectableProbeSN3"
[1] "Creating boxplot for Raw_tissue  ..."
[1] "Creating correlation matrix and plot Raw_tissue  ..."
[1] "Creating detection concordance plot Raw_tissue ..."
Perform Average imputation for probes with FLAG > 5000

quantile normalized data was saved to:
      Result_tissue/DataResult/Expression_quantileNormalized.csv

The expression data object was saved to R workspace file:
      hfe1_design_eset_quantile07Feb2007.Rdata

Perform data analysis on quantile normalized data ...
[1] "Creating boxplot for quantile_tissue  ..."
[1] "Creating MA plot for quantile_tissue"
Error in doPlotEset(esetUse, group, name = normUse, test = test, ...) :
	could not find function "bmp"
 >


ABarray stops at this point. The documentation makes no mention of  
"function bmp" or any possible troubleshooting options. My guess is  
that it is trying to generate .bmp images for the plots immediately  
prior to the error message but I may be mistaken on that. Googling  
and searching the mailing list on that assumption revealed a few  
possible leads, including installing Ghostscript. I have installed  
Ghostscript and include the "Sys.putenv" command at the beginning of  
my R sessions to make sure that R is looking for Ghostscript in the  
correct place. I have a co-worker who has ABarray running correctly  
on his computer (a Windows box), and while I can use his system to  
get some of these analyses done quickly, I  would much rather be able  
to run this on my own desktop machine.

I am using a Power Mac G5 (PowerPC processors), OS X 10.4.8, R  
version 2.4.1, BioC 1.9, and Ghostscript 8.54. I have X11 active  
while using R.

Advice of any sort would be greatly appreciated, and again, I hope I  
have not improperly used the BioConductor list with this request for  
assistance. Thank you in advance!



Alison Ziesel
Department of Ophthalmology, Emory University
aziesel at emory.edu