[BioC] read.maimages & wt.fun

[Martin Morgan]

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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