outlierPlot {beadarray} | R Documentation

## Locations of outliers on an Illumina chip

### Description

Diagnostic function that reports how many outliers are found on a specific array on a chip. We take advantage of the segmental structure of the array and break-down the number of outliers into 9 sections.

### Usage

    outlierPlot(BLData, array = array, log = FALSE, plot = FALSE)

### Arguments

`BLData` | A BeadLevelList object containing the bead-level data for an Illumina experiment
`array` | The number of the array of interest
`log` | if TRUE calculate outliers on the log2 scale. If FALSE calculate outliers on the original scale
`plot` | if TRUE a diagnostic plot will be produced, otherwise only the numbers of outliers will be returned.

### Details

The number of outliers are computed for the whole array using the Illumina default method that specifies a cut-off of 3 MADs from the median on either the log2 or original scale. These outliers are then split into 9 different sections on the array (the separation between these sections can usually be seen in the plots).

### Author(s)

Mark Dunning

[Package beadarray version 1.12.1 Index]