[BioC] read.maimages & wt.fun

[gb606342000]

Hi Martin,

I could solve the problem by running 

Sys.setlocale(locale="C")

Just with that the code is working fine.

Thank you very much for your help :-)

Giovani

--- On Sat, 9/5/09, Martin Morgan <mtmorgan at fhcrc.org> wrote:

> From: Martin Morgan <mtmorgan at fhcrc.org>
> Subject: Re: [BioC] read.maimages & wt.fun
> To: "gb606342000" <gb606342000 at yahoo.com>
> Cc: bioconductor at stat.math.ethz.ch
> Date: Saturday, September 5, 2009, 11:04 AM
> gb606342000 wrote:
> > Dear All,
> 
> Hi Giovani --
> 
> > 
> > I am having problems to import genepix files. Does
> anyone have
> > an idea what is going on? I use Mac OS X version
> 10.5.8.
> > 
> > Please, see below.
> > 
> > Thanks. Giovani
> > 
> > 
> > This code DO NOT work:
> >> f <- function(x) as.numeric(x$Flags > -1) 
> >> RG <- read.maimages(targets, source =
> "genepix", other.columns=list("Flags"), wt.fun = f)
> > Error in gsub("\\.", "\\\\.", x) : 
> >   input string 1 is invalid in this
> locale
> 
> You might arrange for your R to be the 'C' or 'en_US'
> locale, either with
> 
>   Sys.setlocale(locale="C")
> 
> or (whether Sys.setlocale works seems to depend on OS),
> better, when you
> start R (in a bash shell this might be LC_ALL="C" R). I
> think the
> problem is that, in the en_US.UTF-8 locale, a '^2' is
> interpreted as a
> special symbol, not as two ascii characters.
> 
> There's a long and probably more confusing than helpful
> post at
> 
> https://stat.ethz.ch/pipermail/bioconductor/2007-July/018204.html
> 
> Martin
> 
> 
> > Removing the "wt.fun = f", works fine:
> >> f <- function(x) as.numeric(x$Flags > -1) 
> >> RG <- read.maimages(targets, source =
> "genepix",  other.columns=list("Flags"))
> > Read
> 2009_04_02_4805_AXONe_PMT_Cy5_700_Cy3_0450_Lines_avg_0001.gpr
> 
> > Read
> 2009_05_08_4835g_AXON_PMT_Cy5_650_Cy3_0500_Lines_avg_0002_Multi.gpr
> 
> > 
> >> sessionInfo()
> > R version 2.9.2 (2009-08-24) 
> > i386-apple-darwin8.11.1 
> > 
> > locale:
> > en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> > 
> > attached base packages:
> > [1] stats     graphics 
> grDevices utils     datasets 
> methods  
> > [7] base     
> > 
> > other attached packages:
> > [1] limma_2.18.3  marray_1.22.0
> > 
> > loaded via a namespace (and not attached):
> > [1] tools_2.9.2
> > 
> > _______________________________________________
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> 
>