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

[Yue Li]

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")
>> 
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> 
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>