[BioC] marray: problems loading genepix-files

[Heike Pospisil]

Hello again,

as already mentioned in the thread 'Help with GenePix files' the import 
of my genepix files using the marray package failed.

With this post, I am sending the output of sessionInfo() and traceback() 
just after getting the error message.

Thanks a lot for any suggestion and best wishes,
Heike

#################################################################
 > myTargetsa <- read.marrayInfo(file.path(data.dir, "targeta.txt"))
 > galinfo<-read.Galfile("3kArray5.gal")
 > 
data<-read.GenePix(c("a.gpr","ar.gpr"),targets=myTargetsa,layout=galinfo$layout,gnames=galinfo$gnames,)

Reading ...  a.gpr
Error in if (skip > 0) readLines(file, skip) :
         missing value where TRUE/FALSE needed
#################################################################
 > traceback()
4: read.table(f, skip = skip2, header = TRUE, sep = sep, quote = quote,
        check.names = FALSE, as.is = TRUE, comment.char = "", nrows = 
nspots,
        ...)
3: read.marrayRaw(fnames = c("a.gpr", "ar.gpr"), name.Gf = "F532 Median",
        name.Gb = "B532 Median", name.Rf = "F635 Median", name.Rb = 
"B635 Median",
        name.W = "Flags", layout = <S4 object of class "marrayLayout">,
        gnames = <S4 object of class "marrayInfo">, targets = <S4 object 
of class "marrayInfo">,
        notes = "GenePix Data", sep = "\t", quote = "\"", DEBUG = FALSE,
        path = NULL, skip = NULL, fill = TRUE)
2: do.call("read.marrayRaw", maRaw.args)
1: read.GenePix(c("a.gpr", "ar.gpr"), targets = myTargetsa, layout = 
galinfo$layout,
        gnames = galinfo$gnames, )
#################################################################
 > sessionInfo()
R version 2.4.1 (2006-12-18)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US.ISO-8859-1;LC_NUMERIC=C;LC_TIME=en_US.ISO-8859-1;LC_COLLATE=en_US.ISO-8859-1;LC_MONETARY=en_US.ISO-8859-1;LC_MESSAGES=en_US.ISO-8859-1;LC_PAPER=en_US.ISO-8859-1;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.ISO-8859-1;LC_IDENTIFICATION=C

attached base packages:
[1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"
[7] "base"

other attached packages:
   marray    limma
"1.12.0"  "2.8.1"

-- 
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