[BioC] Help with GenePix files

[Heike Pospisil]

Hello,

it's the first time I am dealing with two-color microarrays. That is why 
I have some (probably stupid) questions...

I am trying to analyze GenePix files using the marrayInput package and I 
ran into two difficulties:

1) I have 24 GenePix-arrays that are defined by three different 
*.gal-files. Can I merge the expressions for these three types of arrays 
for the upcoming normalization step?

2) Does someone know the error message "Error in if (skip > 0) 
readLines(file, skip) : missing value where TRUE/FALSE needed" and has a 
hint for avoiding it?

 > galinfo<-read.Galfile("3kArray5.gal")
 > myTargets <- read.marrayInfo(file.path(data.dir, "target.txt"))
target.txt:
   Name   Cy3 Cy5
  a.gpr   10D 14D
ar.gpr   14D 10D
 > 
read.GenePix(c("a.gpr","ar.gpr"),targets=myTargets,layout=galinfo$layout,gnames=galinfo$gnames,) 


Reading ...  a.gpr
Error in if (skip > 0) readLines(file, skip) :
         missing value where TRUE/FALSE needed

Unfortunately, I have no idea what could be the reason for this error 
message. I would be very glad about any suggestion.

Thanks in advance and best wishes,
Heike

PS: I am using R2.3.1 and marray version 1.12.0.
-- 
Dr. Heike Pospisil      | pospisil at zbh.uni-hamburg.de
University of Hamburg   | Center for Bioinformatics
Bundesstrasse 43        | 20146 Hamburg, Germany
phone:+49-40-42838-7303 | fax: +49-40-42838-7312