plotXY {beadarray}R Documentation

XY plots for two samples

Description

Function to display an XY plot of the average values of genes from two different samples or from two channels from the same array.

If two array indices are given as parameters then two arrays will be compared, otherwise the red and green channels from one array will be plotted

Usage

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

Arguments

exprs expression matrix from an ExpressionSet or eSet object
array1 numeric value for the first sample to be plotted
array2 numeric value for the second sample to be plotted
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 intensity versus the array2 intensity for each gene.

Value

Plot will be produced on the current graphical device

Author(s)

Mark Dunning

Examples

data(BSData)

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

[Package beadarray version 1.6.0 Index]