plotBeadIntensities {beadarray}R Documentation

Plot bead intensities

Description

Function to plot the intensities of all beads of a particular type on an array.

Usage

plotBeadIntensities(BLData, ProbeIDs, arrays, log = FALSE,
          whatToPlot="G", ProbeCols=NULL, ylim=NULL,...)

Arguments

BLData a BeadLevelList object
ProbeIDs numeric value giving the ProbeID(s) for the bead type(s) we are interested in
arrays numeric value giving the array we are interested in
log if TRUE log2 intensities are plotted (and used to find outliers)
whatToPlot character string specifying which intensities to plot. Possibilities are "G", "Gb" for single channel data and "G", "Gb", "R" and "Rb" for two-colour data
ProbeCols vector of colour names to assign to each bead type
ylim vector providing the upper and lower bounds for the y-axis in the plotting window
... further graphical parameters to plot

Details

Boxplots of the G, Gb, R or Rb intensities on the original or log-scale for each bead type specified by ProbeIDs on selected arrays is produced.

Value

Plot is produced on current graphical device

Author(s)

Mark Dunning

Examples

data(BLData)

plotBeadIntensities(BLData, arrays=seq(1:4), ProbeIDs=c(2,1000), log=TRUE)

[Package beadarray version 1.6.0 Index]