poscontPlot: Plot the positive controls

In markdunning/beadarray-devel: Quality assessment and low-level analysis for Illumina BeadArray data

Description

Function for retrieving and plotting the biotin and housekeeping controls for an expression array. We know these controls should show high signal and are therefore useful for QA purposes. The housekeeping control targets a bead-type believed to be universally expressed whereas the biotin control targets the biotin used for staining.

Usage

poscontPlot(BLData, array = 1, transFun = logGreenChannelTransform, positiveControlTags = c("housekeeping", "biotin"), colList = c("red", "blue"), controlProfile = NULL, ...)

Arguments

BLData	a beadLevelData object
array	The section to be plotted
transFun	What transformation function to be applied prior to plotting
positiveControlTags	What identifiers to be used as positive controls
colList	vector of colours to be used to each positive control
controlProfile	an optional data frame with columns defining the ArrayAddress IDs and control\-type for all controls on the platform.
...	other arguments to plot

Details

Function for plotting the observed intensites for all replicates of the specified control probes on a given array\-section. The identity of the control probes can be specified by passing a ControlProfile data frame, with the first column being a vector of ArrayAddress IDs and the second column being a corresponding set of characters tags. The beads to be plotted are found by matching the positiveControlTags argument to these character tags. Users with expression data can have the ControlProfile data frame defining automatically within the function, provided the annotation of the beadLevelData object has been defined by readIllumina or setAnnotation.

Value

Plot to current graphical device

Author(s)

Mark Dunning

References

www.illumina.com/downloads/GX\_QualityControl\_TechNote.pdf

Examples

###Load the example beadLevelData and associated controlProfile

if(require(beadarrayExampleData)){


data(exampleBLData)

poscontPlot(exampleBLData, array=1)

poscontPlot(exampleBLData, array=2)

}

markdunning/beadarray-devel documentation built on May 21, 2019, noon