Question: images of affyPLM package in R 2.7.2
0
gravatar for Hui-Yi Chu
11.2 years ago by
Hui-Yi Chu160
Hui-Yi Chu160 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]]
• 681 views
ADD COMMENTlink modified 11.2 years ago by Ben Bolstad1.2k • written 11.2 years ago by Hui-Yi Chu160
Answer: images of affyPLM package in R 2.7.2
0
gravatar for Ben Bolstad
11.2 years ago by
Ben Bolstad1.2k
Ben Bolstad1.2k 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.u tf8;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_IDENTIFICATI ON=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
ADD COMMENTlink written 11.2 years ago by Ben Bolstad1.2k
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 >
ADD REPLYlink written 11.2 years ago by Henrik Bengtsson2.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 197 users visited in the last hour