limma (version 3.22.7)

plotMA: MA-Plot

Description

Creates an MA-plot with color coding for control spots.

Usage

"plotMA"(object, array = 1, xlab = "Average log-expression", ylab = "Expression log-ratio (this sample vs others)", main = colnames(object)[array], status=NULL, ...)
"plotMA"(object, array = 1, xlab = "Average log-expression", ylab = "Expression log-ratio (this sample vs others)", main = colnames(object)[array], status=object$genes$Status, zero.weights = FALSE, ...)
"plotMA"(object, array = 1, xlab = "A", ylab = "M", main = colnames(object)[array], status=object$genes$Status, zero.weights = FALSE, ...)
"plotMA"(object, array = 1, xlab = "A", ylab = "M", main = colnames(object)[array], status=object$genes$Status, zero.weights = FALSE, ...)
"plotMA"(object, coef = ncol(object), xlab = "Average log-expression", ylab = "log-fold-change", main = colnames(object)[coef], status=object$genes$Status, zero.weights = FALSE, ...)

Arguments

object

an RGList, MAList, EList, ExpressionSet or MArrayLM object. Alternatively a numeric matrix.

array

integer giving the array to be plotted.

coef

integer giving the linear model coefficient to be plotted.

xlab

character string giving label for x-axis

ylab

character string giving label for y-axis

main

character string giving title for plot

status

vector giving the control status of each spot on the array, of same length as the number of rows of object. If NULL, then all points are plotted in the default color, symbol and size.

zero.weights

logical, should spots with zero or negative weights be plotted?

...

other arguments are passed to plotWithHighlights.

Value

Details

An MA-plot is a plot of log-intensity ratios (M-values) versus log-intensity averages (A-values). For two color data objects, a within-array MA-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, then a between-array MA-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 MA-plot in which the estimated coefficient is on the y-axis and the average A-value is on the x-axis.

The status vector is intended to specify the control status of each spot, for example "gene", "ratio control", "house keeping gene", "buffer" and so on. The vector is often computed using the function controlStatus and a spot-types file. However the function may be used to highlight any subset of spots.

The status can be included as the component object$genes$Status instead of being passed as an argument to plotMA. The arguments values, pch, col and cex can be included as attributes to status instead of being passed as arguments to plotMA.

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 43, doi: 10.1093/nar/gkv007.

See Also

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

Examples

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")
col <- c("blue","red","green")

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

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

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

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