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

In markdunning/beadarray-devel: Quality assessment and low-level analysis for Illumina BeadArray data

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.

Author(s)

Mark Dunning

Examples

if(require(beadarrayExampleData)){

data(exampleSummaryData)

plotMAXY(exprs(channel(exampleSummaryData, "G")), arrays=1:3, log=FALSE)

}

markdunning/beadarray-devel documentation built on May 21, 2019, noon