backgroundControlPlot {beadarray}R Documentation

QA measures based on bead-level negative controls

Description

Function for plotting the bead-level intensities for all the negative controls that are placed on an array. Typically there are around a thousand of these controls, each replicated 30 times. The sequences used for these controls should not target any part of the genome and therefore we should not observe any signal.

Usage

backgroundControlPlot(BLData, array = 1, plot = FALSE)

Arguments

BLData A BeadLevelList for an Illumina expression chip
array The number of the array in BLData that we want QA of.
plot if TRUE a diagnostic plot will be produced

Details

For QA, we report the mean and variance of all negative controls (of all bead-types) after first removing outiers using a 3 MAD cut-off. To retrieve the IDs of the negative controls, we make use of the annotation slot stored with the BeadLevelList object. It is therefore important that this information is accurate. A plot of all negative control bead-types can also be produced, where each bead-type is represented by a vertical line covering the inter-quartile range and ordered according to mean intensity. Too many high intensity values for the negatives could indicate a poor quality array.

Value

The function returns the mean (AveNeg) and variance (VarNeg) of all negative control beads and a diagnositc plot if requested.

Author(s)

Mark Dunning and Andy Lynch

See Also

calculateBeadLevelScores


[Package beadarray version 1.10.0 Index]