plotXY.beads {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.beads(BSData, array1, array2 = 0, log = FALSE, identify = FALSE,
label = FALSE, fold = 2, highlight = NULL, sampleSize = NULL,...)

Arguments

BSData BeadSummaryList object
array1 numeric value for the first sample to be plotted
array2 numeric value for the second sample to be plotted
log if TRUE all data will be log2-transformed
identify if TRUE the user will be able to find additional information about each point by clicking on it
label if TRUE the position of control types will be shown on the plot
fold numeric value specifying what fold change lines to display on the plot
highlight vector of numeric values that the user wishes to be highlighted
sampleSize Defines the number of genes to plot. Default is NULL, which plots everything
... 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 1.0.0 Index]