See the currently running r-help thread '"figure margins too large" issue' started yesterday. That seems to have a likely explanation for the updates in R causing this; it seems that the default image *dimensions* (not parameter 'mar') have changed. My $.02 /Henrik On Wed, Sep 10, 2008 at 7:21 AM, Ben Bolstad <bmb at="" bmbolstad.com=""> wrote: > As far as I a can recall no such changes have been made to this function > in the last several BioC releases. Additionally, testing this on my > machine is showing no such issues. > > What chip type are you working with? Also your sessionInfo() don't show > the versions of affyPLM etc that you are using. > > Ben > >> library(affyPLM) > Loading required package: affy > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: affyio > Loading required package: preprocessCore > Loading required package: gcrma > Loading required package: matchprobes > Loading required package: splines >> library(affydata) >> data(Dilution) >> Pset <- fitPLM(Dilution) >> image(Pset, which = 1, type = "resids", > + col = pseudoPalette(low = "darkgreen",high = "red", mid = > "white"), > + add.legend = TRUE) >> sessionInfo() > R version 2.7.2 (2008-08-25) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.utf8;LC_NUMERIC=C;LC_TIME=en_US.utf8;LC_COLLATE=en_US .utf8;LC_MONETARY=C;LC_MESSAGES=en_US.utf8;LC_PAPER=en_US.utf8;LC_NAME =C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.utf8;LC_IDENTIFICA TION=C > > attached base packages: > [1] splines tools stats graphics grDevices utils > datasets > [8] methods base > > other attached packages: > [1] hgu95av2cdf_2.2.0 affydata_1.11.3 affyPLM_1.16.0 > [4] gcrma_2.12.1 matchprobes_1.12.0 affy_1.18.2 > [7] preprocessCore_1.2.0 affyio_1.8.0 Biobase_2.0.1 > > > > > > > > > > > > > On Wed, 2008-09-10 at 09:35 -0400, Hui-Yi Chu wrote: >> Dear list, >> >> I updated R from 2.6.2 to 2.7.2 recently but keep getting the error "figure >> margins too large" when plot pictures which never happened to me when using >> 2.6.2. Also, the legend disappears in R 2.7.2. After asking R mailing list, >> they think it's something specifically changed in image() of affy package, >> especially add.legend argument. But I dont know how to fix it or change the >> settings. Any suggestions are really appreciated!!! >> >> ------------------------------ >> library("affyPLM") >> aaa.qc <- fitPLM(aaa, background=T, normalize=T) ## rma- normalized >> data >> image(aaa.qc, which = 1, type = "resids", >> col = pseudoPalette(low = "darkgreen",high = "red", mid = "white"), >> add.legend = TRUE) >> ------------------------------ >> ps. aaa is an affybatch of raw data >> >> I tried to add par(mar=c(2,2,2,2)) before the image line above to see if >> anything changed, but I still cannot see the legend which is visible in >> R2.6.2. >> >> For more info, following is my two sessions of R. >> *1.* >> R version 2.6.2 (2008-02-08) >> 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 >> >> >> *2.* >> R version 2.7.2 (2008-08-25) >> 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 >> >> >> Thank you in advance!! >> Regards, >> Hui-Yi >> >> [[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 > > _______________________________________________ > 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 >