suppress messages in rma

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Georg Otto ▴ 510

@georg-otto-956

Last seen 10.2 years ago

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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ADD COMMENT • link updated 17.1 years ago by Martin Morgan 25k • written 17.1 years ago by Georg Otto ▴ 510

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Ben Bolstad ★ 1.2k

@ben-bolstad-1494

Last seen 7.3 years ago

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_U S.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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD COMMENT • link 17.1 years ago Ben Bolstad ★ 1.2k

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Martin Morgan 25k

@martin-morgan-1513

Last seen 4 months ago

United States

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.UT F-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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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

ADD COMMENT • link 17.1 years ago Martin Morgan 25k

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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=e n_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 > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor at stat.math.ethz.ch > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/

ADD REPLY • link 17.1 years ago Roger Peng ▴ 10

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