[BioC] problems with marray and gpr files

[Martin Morgan]

Jörg <edd17 at gmx.de> writes:

> Hello,
> I am pretty new to marray and actually having the same problem.
> When using read.GenePix() I get the error
>
> ""Error in if (skip > 0) readLines(file, skip) :
>  >         missing value where TRUE/FALSE needed"
>
> Additionally I get a warning message
>
> ": In grep(layout.id[1], y) :
> Inputstring  30 not valid with this locale."
>
> When using the skip option with the number of row in the header I get
>
> "Error in `[.data.frame`(dat, , info.id) : undefined columns selected"
>
>
>
> I tried different gpr files also files downloaded from:
>
> http://genomebiology.com/2003/4/2/R9/additional/
>
> The columns are named exactly as expected in read.GenePix()
> so I don't think it is a problem with the files.
>
> Here they mention that it might be a problem with R locate:
> https://stat.ethz.ch/pipermail/bioconductor/2005-May/008928.html
>
> Unfortunately I don't know a lot about this.

Can you mention what the output of

> sessionInfo()

is? Also try

> Sys.setlocale(locale="C")

before read.GenePix, and if that does not work try, as you start R
from the command line of your operating system,

% LC_ALL="C" R

It would be good if you could report back to the list whether these
approaches work.

Martin

> My System:
>
> Ubuntu Feisty Fawn, Linux 2.6.24-23-generic i686,
> R version 2.8.1 (also tried older versions), Bioconductor 2.3
>
>
> I would be very grateful for every help or hint.
>
> thanks a lot,
> Jörg
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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