Entering edit mode
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",s
ep="")
> +
> 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. Fern?ndez (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- C?rdoba-5000-Argentina
