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, array, n=3,log=FALSE,label=FALSE,main=NULL,ylim=NULL,...)

### Arguments

`BLData` | BeadLevelList object
`ProbeIDs` | numeric value giving the ProbeID for the bead type we are interested in
`array` | numeric value giving the array we are interested in
`n` | outlier values for the bead type are beads with intensity more than 'n' times away from the mean
`log` | if TRUE log2 intensities of each bead are used to find outliers
`label` | if TRUE all beads will be given a numeric ID on the plot
`ylim` | vector providing the upper and lower bounds for the y-axis in the plotting window
`main` | specify a title for the plot
`...` | further graphical parameters to `plot`

### Details

We find the intensities for each bead of the specified bead type by simply finding the value of BLData$R for each bead in the array whose BLData$ProbeID matches the specified ProbeID. The distance from the centre of the hexagon can be found in a similar fashion by looking at BLData$x and BLData$y.

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)

    #By default, outliers found by Illumina method are highlighted

    plotBeadIntensities(BLData, 2, 1)

    plotBeadIntensities(BLData, 2, 1, log=TRUE)

    plotBeadIntensities(BLData, 2, 1, log=TRUE, n=5)

    #Increasing n selects only the most extreme outliers

    plotBeadIntensities(BLData, 4279, 1, log=TRUE, n=3)

    plotBeadIntensities(BLData, 4279, 1, log=TRUE, n=4.5)

    plotBeadIntensities(BLData, 4279, 1, log=TRUE, n=6)

[Package beadarray version 1.0.0 Index]