[BioC] suppress messages in rma

[Martin Morgan]

but if you insist on quiet ---

> library(affy)
> example(rma)
[snip]
> jnk <- character(0)
> con <- textConnection("jnk", "w")
> sink(con)
> eset <- rma(affybatch.example)
> sink()
> jnk
[1] "Background correcting"  "Normalizing"            "Calculating Expression"

Martin

Ben Bolstad <bmb at bmbolstad.com> writes:

> 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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-- 
Martin Morgan
Computational Biology Shared Resource Director
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793