plotBeadIntensities {beadarray} | R Documentation |
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.
plotBeadIntensities(BLData, ProbeIDs, arrays, log=FALSE, n=3,ProbeCols=NULL,ylim=NULL,...)
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 |
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.
Plot is produced on current graphical device
Mark Dunning
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))