[BioC] marray: problems loading genepix-files

[Jean Yee Hwa Yang]

Hi Heike

I am guessing there is a mismatch between the gal file and the gpr file 
you are reading in.  Usually the first 5 columns of any gpr file is the 
same as the gal file.

Please try the two options and let me know how you go

Option 1
data = read.GenePix(fnames = c("a.gpr", "ar.gpr"))

Option 2
myTargetsa <- read.marrayInfo(file.path(data.dir, "targeta.txt"))
data = read.GenePix(targets = myTargetsa)

Please also show me myTargetsa.  If you have further problems, you are 
welcome to send me a link where I can download your gpr file and take a 
look.

Cheers

Jean


> #################################################################
> > 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, )
> #################################################################