Mean-Difference Plot of Expression Data

Description

Creates a mean-difference plot (aka MA plot) with color coding for highlighted points.

Usage

## Default S3 method:
plotMD(object, column = 1, xlab = "Average log-expression",
       ylab = "Expression log-ratio (this sample vs others)",
       main = colnames(object)[column], status=NULL, ...)
## S3 method for class 'EList'
plotMD(object, column = 1, array = NULL, xlab = "Average log-expression",
       ylab = "Expression log-ratio (this sample vs others)",
       main = colnames(object)[column], status=object$genes$Status,
       zero.weights = FALSE, ...)
## S3 method for class 'RGList'
plotMD(object, column = 1, array = NULL, xlab = "A", ylab = "M",
       main = colnames(object)[column], status=object$genes$Status,
       zero.weights = FALSE, ...)
## S3 method for class 'MAList'
plotMD(object, column = 1, array = NULL, xlab = "A", ylab = "M",
       main = colnames(object)[column], status=object$genes$Status,
       zero.weights = FALSE, ...)
## S3 method for class 'MArrayLM'
plotMD(object, column = ncol(object), coef = NULL, xlab = "Average log-expression",
       ylab = "log-fold-change", main = colnames(object)[column],
       status=object$genes$Status, zero.weights = FALSE, ...)

Arguments

Details

A mean-difference plot (MD-plot) is a plot of log-intensity ratios (differences) versus log-intensity averages (means). For two color data objects, a within-array MD-plot is produced with the M and A values computed from the two channels for the specified array. This is the same as a mean-difference plot (mdplot) with the red and green log2-intensities of the array providing the two columns.

For single channel data objects, a between-array MD-plot is produced. An articifial array is produced by averaging all the arrays other than the array specified. A mean-difference plot is then producing from the specified array and the artificial array. Note that this procedure reduces to an ordinary mean-difference plot when there are just two arrays total.

If object is an MArrayLM object, then the plot is an fitted model MD-plot in which the estimated coefficient is on the y-axis and the average A-value is on the x-axis.

The status vector can correspond to any grouping of the probes that is of interest. If object is a fitted model object, then status vector is often used to indicate statistically significance, so that differentially expressed points are highlighted. If object is a microarray data object, then status might distinguish control probes from regular probes so that different types of controls are highlighted.

The status can be included as the component object$genes$Status instead of being passed as an argument to plotMD.

See plotWithHighlights for how to set colors and graphics parameters for the highlighted and non-highlighted points.

Value

A plot is created on the current graphics device.

Note

This function is an alternative to plotMA, which was one of the original functions of the limma package in 2002. The history of mean-difference plots and MA-plots is reviewed in Ritchie et al (2015).

Author(s)

Gordon Smyth

References

Ritchie, ME, Phipson, B, Wu, D, Hu, Y, Law, CW, Shi, W, and Smyth, GK (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research Volume 43, e47. http://nar.oxfordjournals.org/content/43/7/e47

See Also

The driver function for plotMD is plotWithHighlights. See also mdplot for a very basic mean-difference plot function.

An overview of plot functions available in LIMMA is given in 09.Diagnostics.

Examples

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)

#  Same as above but setting graphical parameters as attributes
attr(status,"values") <- values
attr(status,"col") <- hl.col
plotMD(MA, main="Mean-Difference Plot with 12 spiked-in points", status=status)

#  Same as above but passing status as part of object
MA$genes$Status <- status
plotMD(MA, main="Mean-Difference Plot with 12 spiked-in points")

#  Change settings for background points
MA$genes$Status <- status
plotMD(MA, bg.pch=1, bg.cex=0.5)