plotBeadIntensities {beadarray} | R Documentation

## Plot bead intensities

### Description

Function to plot the intensities of all beads of a particular type on an array against their distance from the centre of the array. Any outliers for the bead type will be highlighted.

### Usage

    plotBeadIntensities(BLData, ProbeIDs, arrays, log = FALSE, n=3,
              whatToPlot="G", ProbeCols=NULL, ylim=NULL,...)

### Arguments

`BLData` | a BeadLevelList object
`ProbeIDs` | numeric value giving the ProbeID for the bead type 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)
`n` | outlier values for the bead type are beads with intensity more than 'n' times away from the mean
`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

We find the intensities for each bead of the specified bead type by finding the G, Gb, R or Rb intensities for each bead in the array whose BLData$ProbeID matches the specified ProbeID. The distance from the centre of the hexagon can be found in a similar fashion by looking at the GrnX and GrnY values.

The outliers for the bead type are beads which have intensity more than 'n' times away from the standard deviation using logged or un-logged bead intensities (specified using 'log' argument).

The mean for the bead type and lines 3 standard deviations from the mean are shown on the plot.

### 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 1.4.0 Index]