Apparently limma_3.18.13 fixed the bug! Thanks again. On Mar 28, 2014, at 4:54 PM, Yue Li <gorillayue@gmail.com> wrote: > Thanks Jim. I am upgrading all of my installed bioc packages. It's likely to just be the transient bug from the old version of limma package like you mentioned. > > > On Mar 28, 2014, at 4:51 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > >> Hi Yue, >> >> Here is what I get: >> >> > library(limma) >> > png("tmp.png") >> > MA <- new("MAList") >> > MA$A <- runif(300,4,16) >> > MA$M <- rt(300,df=3) >> > status <- rep("Gene",300) >> > status[1:3] <- "M=0" >> > MA$M[1:3] <- 0 >> > status[4:6] <- "M=3" >> > MA$M[4:6] <- 3 >> > status[7:9] <- "M=-3" >> > MA$M[7:9] <- -3 >> > plotMA(MA,main="MA-Plot with Simulated Data",status=status,values =c("M=0","M=3","M=-3"),col=c("blue","red","green")) >> > dev.off() >> null device >> 1 >> > png("tmp2.png") >> > plotMA(MA,main="MA-Plot with Simulated Data",status=status,values =c("M=0","M=3","M=-3"),col=c("blue","red","green"), xlab="A") >> > dev.off() >> X11cairo >> 2 >> > sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] limma_3.18.13 >> >> And see attached. You have an outdated version of limma, so try updating. >> >> Best, >> >> Jim >> >> >> >> On Fri, Mar 28, 2014 at 1:44 PM, Yue Li <gorillayue@gmail.com> wrote: >> Hi Jim, >> >> I tried it on both my Mac and Linux server and observed the same outcomes. Here are the session info. >> >> Mac: >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] limma_3.18.0 >> >> >> >> Linux: >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 >> [5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=C >> [7] LC_PAPER=en_CA.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] BiocInstaller_1.12.0 >> >> >> >> On Mar 28, 2014, at 4:31 PM, James W. MacDonald <jmacdon@uw.edu> wrote: >> >> > Hi Yue, >> > >> > I don't see that. Note that it is important to also include the output from sessionInfo() so people know which version of packages you are using. This may have been a transient bug that was already fixed. >> > >> > What is your sessionInfo()? >> > >> > Best, >> > >> > Jim >> > >> > >> > On 3/28/2014 4:25 PM, Yue Li wrote: >> >> Dear List, >> >> >> >> Somehow the plotMA function in limma package labels both x and y-axis title as 'M', where x-axis title should have been "A". >> >> >> >> The function resist the changes I try to make by setting the xlab in the plotMA function. See example below. >> >> >> >> I wonder if anyone came across the same thing and found an easy fix for this "bug". >> >> >> >> Thanks in advance, >> >> Yue >> >> >> >> MA <- new("MAList") >> >> MA$A <- runif(300,4,16) >> >> MA$M <- rt(300,df=3) >> >> status <- rep("Gene",300) >> >> status[1:3] <- "M=0" >> >> MA$M[1:3] <- 0 >> >> status[4:6] <- "M=3" >> >> MA$M[4:6] <- 3 >> >> status[7:9] <- "M=-3" >> >> MA$M[7:9] <- -3 >> >> plotMA(MA,main="MA-Plot with Simulated Data",status=status,value s=c("M=0","M=3","M=-3"),col=c("blue","red","green")) >> >> >> >> >> >> # same label >> >> plotMA(MA,main="MA-Plot with Simulated Data",status=status,value s=c("M=0","M=3","M=-3"),col=c("blue","red","green"), xlab="A") >> >> >> >> _______________________________________________ >> >> Bioconductor mailing list >> >> Bioconductor@r-project.org >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> > -- >> > James W. MacDonald, M.S. >> > Biostatistician >> > University of Washington >> > Environmental and Occupational Health Sciences >> > 4225 Roosevelt Way NE, # 100 >> > Seattle WA 98105-6099 >> > >> >> >> <tmp.png><tmp2.png> > [[alternative HTML version deleted]]