beadarray (version 2.22.2)

plotMAXY: Scatter plots and MA-plots for all specified arrays

Description

Produces smoothed scatter plots of M versus A and X versus Y for all pairwise comparisons from a set of arrays.

Usage

plotMAXY(exprs, arrays, log = TRUE, genesToLabel=NULL, labels=colnames(exprs)[arrays],labelCol="red", labelpch=16,foldLine=2,sampleSize=NULL,...)

Arguments

exprs

a matrix of expression values

arrays

integer vector giving the indices of the arrays (columns of exprs) to plot

log

if TRUE then all values will be log2-transformed before plotting

genesToLabel

vector of genes to highlight on the plot. These must match the rownames of exprs.

labels

vector of array names to display on the plot

labelCol

plotting colours for highlighted genes

labelpch

plotting characters for highlighted genes

foldLine

a numeric value defining where to draw horizontal fold change lines on the plot

sampleSize

The number of genes to plot. Default is NULL, which plots every gene

...

other graphical parameters to be passed

Details

This graphical tool shows differences that exist between two arrays and can be used to highlight biases between arrays as well as highlighting genes which are differentially expressed. For each bead type, we calculate the average (log2) intensity and difference in intensity (log2-ratio) for each pair of arrays.

In the lower-left section of the plot we see XY plots of the intensities for all pairwise comparisons between the arrays and in the upper right we have pairwise MA plots. Going down the first column we observe XY plots of array 1 against array 2 and array 1 against array 3 etc. Similarly, in the upper-right corner we can observe pairwise MA plots.

Examples

##This function is to be replaced. Please see plotMA