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Hi Artur It looks like 'consensus' uses (in plot.consensus.kmeans) the command get(getOption("device"))() at the start of it's plotting routine. So try > options(device="pdf") > consensus(<your args="" here="">) > dev.off() once you've navigated R's concept of its working directory (using setwd) to point to where you'd like the pdf to be saved. It will create a file Rplots.pdf. (you could get fancier here, writing your own function as a kind of pseudo-device to forward the right arguments to pdf, mypdf=function() pdf("testfile.pdf") and set options(device="mypdf")). Not sure why maanova does things this way, or whether this will work for all plots. Also it's the 'maanova' package. Hope that helps Martin "Artur Veloso" <abveloso at="" gmail.com=""> writes: > Dear all, > > I am using the MAANOVA package to create k-means clusters and wanted to save > the graphs produced by the function "consensus" in a PDF file. I don't get > any error messages when I write my code, but when I try to open the file I > get a message that it can't be opened because there are no pages in the > document. Am I doing something wrong? Does anyone know of a way to go around > this? > > Thanks a lot! > > Artur Veloso > Masters in Marine Biology Candidate > College of Charleston, South Carolina > > # this works fine, so I don't think the problem is creating the pdf file > pdf("test_file.pdf") > plot(1:10,1:10) > dev.off() > > # this also works, but the pdf file does not get the consensus plot > library(maanova) > dolphin.maanova <- read.madata > ("maanova_males_data.txt","maanova_males_design.txt",arrayType="oneC olor", > probeid=1,intensity=2) > dolphin.maanova.fit <- fitmaanova(madata=dolphin.maanova,formula=~+Sample) > genes <- read.csv("bioc.males.numbers.csv",header=T) > genes.cluster <- macluster(dolphin.maanova.fit,term="Sample" , > idx.gene=genes[,2],what="gene",method="kmean",kmean.ngroup=8) > pdf("teste.pdf") > bioc.males.consensus <- consensus(bioc.males.cluster,0.5) > dev.off() > > >> sessionInfo() > R version 2.6.1 (2007-11-26) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] maanova_1.8.0 > > loaded via a namespace (and not attached): > [1] tools_2.6.1 > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793