HULK {beadarray}R Documentation

HULK - Bead Array Normalization by NEighbourhood Residuals

Description

Normalizes an probe intensities by calculating a weighted average residual based on the residuals of the surrounding probes.

Usage

HULK(BLData, array, neighbours = NULL, invasions = 20, what = "G")

Arguments

BLData BeadLevelList
array integer specifying which strip/array to plot
neighbours A Neighbours matrix. Optional - if left NULL, it will be computed.
invasions Integer - Number of invasions used when identifying neighbouring beads.
what Specify the data in the BLData to create the residuals from. Defaults to the foreground intensities of the green channel.

Details

HULK is a method of intensity normalization based upon the BASH framework. Firstly For each bead a local neighbourhood of beads is determined, using the same process as the other BASH functions.

For each bead a weighted average residual is calculated. The average residual is calculated as the sum of the residuals for each bead in the neighbourhood, divided by 1 plus the number of invasions it took to reach that bead. This calculation is made by a call to HULKResids.

The average residuals are then subtracted from each bead and the resulting BeadLevelList object is returned.

Value

An object of class BeadLevelList

Author(s)

Mike Smith

References

Cairns JM, Dunning MJ, Ritchie ME, Russell R, Lynch AG. (2008). BASH: a tool for managing BeadArray spatial artefacts. Bioinformatics, 24(24):2921-2.

See Also

HULKResids, BASH

Examples

data(BLData)
o <- HULK(BLData, 1)

[Package beadarray version 1.12.1 Index]