How to adjust FDR in plotMD?

Question

[tanya_fiskur]

Hi everyone.

Is it possible to adjust FDR in plotMD? There is no such function in the command description (https://www.rdocumentation.org/packages/limma/versions/3.28.14/topics/plotMD ), but it's quite necessary.

Thanks for any help!

Answer 1

[Kevin Blighe]

Hey Tanya,

There is no filtering occurring in limma::plotMD() with regard to p-values. The function produces a plot for log mean (x-axis) versus log ratio (y-axis).

However, there is functonality provided that permits you to colour shade certain points, e.g., those genes that pass, e.g., 5% FDR. Taking the example from the manual page:

require(limma)
A <- runif(1000,4,16)
y <- A + matrix(rnorm(1000*3,sd=0.2),1000,3)
status <- rep(c(0,-1,1),c(950,40,10))
y[,1] <- y[,1] + status
plotMD(y, column=1, status=status, values=c(-1,1), hl.col=c("blue","red"))

MA <- new("MAList")
MA$A <- runif(300,4,16)
MA$M <- rt(300,df=3)

# Spike-in values
MA$M[1:3] <- 0
MA$M[4:6] <- 3
MA$M[7:9] <- -3

status <- rep("Gene",300)
status[1:3] <- "M=0"
status[4:6] <- "M=3"
status[7:9] <- "M=-3"
values <- c("M=0","M=3","M=-3")
hl.col <- c("blue","red","green")

plotMD(MA,main="MA-Plot with 12 spiked-in points",
       status=status, values=values, hl.col=hl.col)

Take a closer look at the status, values, and hl.col variables, and then I am sure that you will figure it out.

Kevin

[tanya_fiskur]

Kevin, thank you very much! You helped me many times already :). I tried, but by now it looks like this: https://ibb.co/Ws9Xr4r

[Kevin Blighe]

Are you using FPKM expression units?

[tanya_fiskur]

No, it's just EdgeR results after Featurecounts.

[Kevin Blighe]

Cool. You should check to see which genes have those extremely low fold changes and then try to understand if it is a genuine result or not. For example, check that they are not low-expressed genes, which can result in unrealistic fold-changes