[BioC] suppress messages in rma

[Roger Peng]

I think 'capture.output()' might be what's called for here.

-roger

On 10/26/07, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 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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> >
> > _______________________________________________
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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
>
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-- 
Roger D. Peng  |  http://www.biostat.jhsph.edu/~rpeng/