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

[Martin Morgan]

On 03/26/2010 04:09 PM, Gordon K Smyth wrote:
> 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.

Perhaps ?Sys.setlocale within your R session, or setting the appropriate
environment variable before launching R.

Martin

> 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. 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
> 
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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