plotXY {beadarray} | R Documentation

## XY plots for two samples

### Description

Function which produces an XY plot of the intensities from two specified arrays.

### Usage

    plotXY(exprs,array1=1, array2=2, genesToLabel=NULL, labelCol="red", log=TRUE,labelpch=16, foldLine=2,sampleSize=NULL,...)

### Arguments

`exprs` | a matrix of expression values
`array1` | integer specifying the first array to plot
`array2` | integer specifying the second array to plot
`genesToLabel` | vector of genes to highlight on the plot. These must match the rownames of `exprs`.
`labelCol` | plotting colours for highlighted genes
`log` | if TRUE the data will be log-transformed before plotting
`labelpch` | plotting characters for highlighted genes
`foldLine` | a numeric value defining where to fold change lines on the plot
`sampleSize` | The number of genes to plot. Default is NULL, which plots every gene.
`...` | other graphical parameters to plot that can be specified

### Details

Plots the `array1` intensities versus the `array2` intensities for all probes.

### Value

A smoothed scatter plot is displayed on the current graphical device

### Author(s)

Mark Dunning

### Examples

    data(BSData)

    plotXY(exprs(BSData), array1=1, array2=2)

[Package beadarray version 1.12.1 Index]