[BioC] plotMA {limma} wrong xlab - a bug?

[James W. MacDonald]

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 You have an outdated version of limma, so try updating.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 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
> >
>
>
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