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]