illuminaOutlierMethod {beadarray} | R Documentation

## Identifier outliers on an array section

### Description

Implementation of the illumina method for excluding outliers using a fixed number of MADs (median absolute deviations) cutoff for each bead type

### Usage

    illuminaOutlierMethod(inten, probeList, wts=1, n = 3)

### Arguments

`inten` | a list of intensities
`probeList` | the IDs corresponding to each intensity value
`wts` | Weights associated with beads, indicating those recommended for removal by, for example, `BASH`
`n` | number of MADs cutoff used

### Details

This function is called within the summarisation routine of beadarray to exclude outliers from an array-section prior to summary. The intensities are not assumed to be on any particular scale and can result from any user-defined transformation function.

Beads with weight zero do not contribute to the outlier calling.

### Value

the positions in the original vector that were determined to be outliers

### Author(s)

Mark Dunning

### See Also

`squeezedVarOutlierMethod`

### Examples

    if(require(beadarrayExampleData)){

    data(exampleBLData)

    oList = illuminaOutlierMethod(logGreenChannelTransform(exampleBLData, 1), getBeadData(exampleBLData, array=1, what="ProbeID"))

    }

[Package beadarray version 2.38.0 Index]