Question: plotMA {limma} wrong xlab - a bug?
0
gravatar for Yue Li
5.6 years ago by
Yue Li370
USA
Yue Li370 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$M[7:9] <- -3 plotMA(MA,main="MA-Plot with Simulated Data",status=status,values=c("M =0","M=3","M=-3"),col=c("blue","red","green")) # same label plotMA(MA,main="MA-Plot with Simulated Data",status=status,values=c("M =0","M=3","M=-3"),col=c("blue","red","green"), xlab="A")
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ADD COMMENTlink modified 5.6 years ago by James W. MacDonald51k • written 5.6 years ago by Yue Li370
Answer: plotMA {limma} wrong xlab - a bug?
0
gravatar for James W. MacDonald
5.6 years ago by
United States
James W. MacDonald51k wrote:
Hi Yue, I don't see that. Note that it is important to also include the output from sessionInfo() so people know which version of packages you are using. This may have been a transient bug that was already fixed. What is your sessionInfo()? Best, Jim On 3/28/2014 4:25 PM, Yue Li wrote: > Dear List, > > Somehow the plotMA function in limma package labels both x and y-axis title as 'M', where x-axis title should have been "A". > > The function resist the changes I try to make by setting the xlab in the plotMA function. See example below. > > I wonder if anyone came across the same thing and found an easy fix for this "bug". > > Thanks in advance, > Yue > > MA <- new("MAList") > MA$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,values=c( "M=0","M=3","M=-3"),col=c("blue","red","green")) > > > # same label > 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") > > _______________________________________________ > Bioconductor mailing list > Bioconductor at 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
ADD COMMENTlink written 5.6 years ago by James W. MacDonald51k
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 at="" 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,values=c ("M=0","M=3","M=-3"),col=c("blue","red","green")) >> >> >> # same label >> 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") >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at 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 >
ADD REPLYlink written 5.6 years ago by Yue Li60
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 at="" 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,values=c ("M=0","M=3","M=-3"),col=c("blue","red","green")) >> >> >> # same label >> 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") >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at 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 >
ADD REPLYlink written 5.6 years ago by Yue Li370
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","g reen")) > 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","g reen"), 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 at="" 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 at="" 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,values=c("M=0","M=3","M=-3"),col=c("blue","red", "green")) > >> > >> > >> # same label > >> 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") > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor at 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 > > > > -------------- next part -------------- A non-text attachment was scrubbed... Name: tmp.png Type: image/png Size: 5996 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20140328="" a0a79564="" attachment.png=""> -------------- next part -------------- A non-text attachment was scrubbed... Name: tmp2.png Type: image/png Size: 5996 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20140328="" a0a79564="" attachment-0001.png="">
ADD REPLYlink written 5.6 years ago by James W. MacDonald51k
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,values =c("M=0","M=3","M=-3"),col=c("blue","red","green")) > >> > >> > >> # same label > >> 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") > >> > >> _______________________________________________ > >> 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]]
ADD REPLYlink written 5.6 years ago by Yue Li370
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]]
ADD REPLYlink written 5.6 years ago by Yue Li370
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