squeezedVarOutlierMethod: Identifier outliers on an array section

In markdunning/beadarray-devel: Quality assessment and low-level analysis for Illumina BeadArray data

Description

An outlier calling method that shrinks the observed variance for a bead-type towards the predicted variance based on all bead-types on the array-section.

Usage

squeezedVarOutlierMethod(inten, probeList, wts=1, n = 3, predictNlim=14)

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 SDs cutoff used
predictNlim	how many beads of a bead-type must be present for that bead-type to contribute to prediction of variances?

Details

This function is called within the summarize routine of beadarray to exclude outlying beads 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, however a log-transformation is recommended.

Bead-types that have predictNlim numbers are used to locally regress bead-type precision against bead-type mean, as well as the squared residual error of bead-type precision against bead-type mean. These are then used as prior values for the distribution of precision to feed into a standard Bayesian calcuation to obtain an estimate of the posterior variance.

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)

Andy Lynch

See Also

illuminaOutlierMethod

Examples

if(require(beadarrayExampleData)){

data(exampleBLData)

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

markdunning/beadarray-devel documentation built on May 21, 2019, noon