illuminaOutlierMethod: Identifier outliers on an array section
In beadarray: Quality assessment and low-level analysis for Illumina BeadArray data

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/BASH.R View source: R/outlierMethods.R

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

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

`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

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.

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

Mark Dunning

squeezedVarOutlierMethod

if(require(beadarrayExampleData)){

data(exampleBLData)

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