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

[James W. MacDonald]

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
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Seattle WA 98105-6099