[BioC] suppress messages in rma

[Ben Bolstad]

This is the currently documented behavior for rma():

 verbose: logical value. If 'TRUE' it writes out some messages.
          (Currently ignored)

meaning that varying that argument will have no effect. I will add it to
my list of things to fix, but in the mean time using threestep() from
affyPLM in its place will by default compute RMA expression values
without printing messages.

Best,

Ben





On Thu, 2007-10-25 at 17:14 +0200, Georg Otto wrote:
> Hi,
> 
> 
> 
> 
> how can I suppress the messages printed by the rma function
> (Background correcting....etc), since verbose=FALSE is ignored?
> 
> Best,
> 
> Georg
> 
> > eset<-rma(Data, verbose=FALSE)
> 
> Background correcting
> Normalizing
> Calculating Expression
> 
> > sessionInfo()
> R version 2.6.0 (2007-10-03) 
> x86_64-redhat-linux-gnu 
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods  
> [8] base     
> 
> other attached packages:
> [1] zebrafishcdf_2.0.0   affy_1.16.0          preprocessCore_1.0.0
> [4] affyio_1.6.1         Biobase_1.16.1      
> 
> loaded via a namespace (and not attached):
> [1] simpleaffy_2.14.05
> 
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