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, array2=0, genesToLabel=NULL, labelCol="red", log=TRUE,labelpch=16,identify=FALSE, 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 gene names to highlight on the plot. These must match the rownames of exprs
labelCol vector of characters to plot for the selected genes
log if TRUE the data will be log-transformed before plotting
labelpch if TRUE then a log2 transformation will be applied to the data before plotting
foldLine a numeric value defining where to draw horizontal fold change lines on the plot
identify numeric value specifying what fold change lines to display on the plot
sampleSize numeric specifiying the size of a random sample to be taken rather than plotting every gene
... other graphical parameters that can be sent to plot

Details

A plot will be produced of the average values for each gene found in sample 1 against the averages found in sample 2.

If identify is set to TRUE then clicking on each point will display information about the ProbeID, gene name and values from both samples of the point clicked

Value

Plot will be produced on the current graphical device

Author(s)

Mark Dunning


[Package beadarray version 1.2.2 Index]