[BioC] error in limma read.images in linux ubuntu

[Gordon K Smyth]

Dear Elmer,

This seems to be a locale problem.  I don't know much about locale 
problems, but my understanding is that they arise from using an extended 
ascii character which is understood in one language, but not supported by 
the software you're using.  My guess is that your Windows R is compiled 
for a Spanish locale whereas your Unix version is compiled for US English. 
I'm guessing that your data file or targets file contain some extended 
ascii characters not valid in English.

You might be able to solve the problem by using versions of R compiled for 
your locale. It's hard for me to say more, because it's not really an 
issue with limma, and there isn't any way that I could reproduce your 
problem to examine it.

Best wishes
Gordon

> Date: Thu, 25 Mar 2010 10:05:58 -0300
> From: Elmer Fern?ndez <elmerfer at gmail.com>
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] error in limma read.images in linux ubuntu
> Content-Type: text/plain
>
> Please
> Could anybody tell me what is the problem? It does not happens in windows.
>
> I was revisiting the read.images code and it seems that the problem is
> related to some wt.fun identification or somethig. because it tryes to
> analize the code of the wt.fun function. Am I right?
>
> library(limma)
> + path=paste(base.path,"UCCOR/Investigacion/Osvaldo/Chile/Directa",sep="")
> +
> targetfiles=readTargets("DirectaSinNormal_TargetFile.csv",path=path,sep=",")
> + signal.cols=list(R="F647 Median",Rb="B647 Median",G="F555 Median",Gb="B555
> Median")
> + RG=read.maimages(paste(path,"/",targetfiles$FileName,sep=""),
> + source="genepix.median",quote = "\"'",columns=signal.cols,wt.fun =
> wtflags(0),
> + other.columns="Flags")
>
> Error in gsub("\\.", "\\\\.", x) :
>  input string 1 is invalid in this locale
> Calls: read.maimages ... switch -> read.columns -> grep -> protectMetachar
> -> gsub
>
>
>> sessionInfo()
> R version 2.10.0 (2009-10-26)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8          LC_NUMERIC=C
> LC_TIME=en_US.UTF-8           LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8       LC_MESSAGES=en_US.UTF-8
> LC_PAPER=en_US.UTF-8          LC_NAME=en_US.UTF-8
> [9] LC_ADDRESS=en_US.UTF-8        LC_TELEPHONE=en_US.UTF-8
> LC_MEASUREMENT=en_US.UTF-8    LC_IDENTIFICATION=en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] limma_3.2.1     SystemUtils_1.0 rkward_0.5.1
>
> loaded via a namespace (and not attached):
> [1] tools_2.10.0
>
> -- 
> Elmer A. Fernández (Bioing. PhD)
> Investigador Asistente CONICET - Research Assistant CONICET
> Porf. Inteligencia Artificial -UCC - Prof. Artificial Intelligence @ UCC
> tel: +54-(0)351-4938000 int 145
> Fax: +54-(0)351-4938081
> web page : http://www.uccor.edu.ar/modelo.php?param=3.8.5.15
> http://sites.google.com/site/biologicaldatamininggroup/Home/
> mail address: Camino Alta Gracia Km 7.1/2- Córdoba-5000-Argentina