[BioC] LIMMA (locale problem with read.maimages)

[Gordon K Smyth]

Hi Daniel,

The error message about 'locale' suggests that this is to do with 
conflicts between different language versions of R.

My guess is that you might be using a version of R compiled for a 
non-English language (such as French) but trying to read a GenePix file 
encoded in a way that is not compatible with that language.  If I'm right, 
it's an R issue rather than a limma issue.

You could clarify this by giving us system information:

   sessionInfo()

There are a number of previous posts on these issues, see for example:

https://stat.ethz.ch/pipermail/bioconductor/2007-December/020549.html
https://stat.ethz.ch/pipermail/bioconductor/2007-July/018204.html
https://stat.ethz.ch/pipermail/bioc-devel/2005-April/000070.html

Best wishes
Gordon

> Date: Tue, 22 Feb 2011 15:50:38 -0800
> From: Daniel Fortin <danielfortin86 at hotmail.com>
> To: <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] LIMMA
>
> I have a problem when running LIMMA. I get the following error message:
> Error in grep(protectMetachar(allcnames[i]), text.to.search) :
>  regular expression is invalid in this locale
> Calls: read.maimages -> read.columns -> grep
>
> The code is below:
>
>> library(limma)
>>
>> targets <-readTargets(file="Targets.txt")
>> RG <-read.maimages(targets$Filename, source="genepix",wt.fun=wtflags(weight=0,cutoff=-50))
>
> Does anyone know how to fix this error?
>
> Thanks,
>
> D

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