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

Yue Li gorillayue at gmail.com
Fri Mar 28 21:25:57 CET 2014

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,

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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