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,ProbeCols=NULL,ylim=NULL,...)

Arguments

BLData 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 of each bead are used to find outliers
n outlier values for the bead type are beads with intensity more than 'n' times away from the mean
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 simply finding the value of BLData$G for each bead in the array whose BLData$ProbeID matches the specified ProbeID. The distance from the centre of the hexagon can be found in a similar fashion by looking at BLData$GrnX and BLData$GrnY.

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

ids = intersect(BLData@ProbeID[,1], BLData@ProbeID[,3])[1:10]

plotBeadIntensities(BLData, ProbeIDs=ids[1], arrays=1, ylim=range(9,11))

plotBeadIntensities(BLData, ProbeIDs=ids[1], arrays=c(1,3), ylim=range(9,11))

plotBeadIntensities(BLData, ProbeIDs=ids, arrays=c(1,3), ylim=range(9,11))


[Package beadarray version 1.2.2 Index]