beadarray (version 2.22.2)

illuminaOutlierMethod: 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

Value

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

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.

See Also

squeezedVarOutlierMethod

Examples

if(require(beadarrayExampleData)){

data(exampleBLData)

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