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 = 1, neighbours = NULL, invasions = 20, useLocs = TRUE, weightName = "wts", transFun = logGreenChannelTransform, outlierFun = illuminaOutlierMethod)

### Arguments

`BLData` | An object of class `beadLevelData-class`
`array` | integer specifying which section/array to process
`neighbours` | A Neighbours matrix. Optional - if left NULL, it will be computed.
`invasions` | Integer - Number of invasions used when identifying neighbouring beads.
`useLocs` | If information from an associated .locs file is to be used. If available using a .locs file can improve both the speed and accuracy of determining the network of neighbouring beads.
`weightName` | Column name where bead weights are to be taken from.
`transFun` | Transformation function.
`outlierFun` | Name or definition for the function to be used to calculated outliers.

### 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 a vector of the resulting corrected intensities object is returned. These corrected intensities can be saved in the original beadLevelData object using `insertBeadData`

### Value

A vector of corrected intensities.

### Author(s)

Mike Smith

### References

Lynch AG, Smith ML, Dunning MJ, Cairns JM, Barbosa-Morais NL, Tavare S. beadarray, BASH and HULK - tools to increase the value of Illumina BeadArray experiments. In A. Gusnato, K.V. Mardia, & C.J. Fallaize (eds), Statistical Tools for Challenges in Bioinformatics. 2009 pp. 33-37. Leeds, Leeds University Press.

### See Also

`BASH`, `insertBeadData`, `logGreenChannelTransform`, `squeezedVarOutlierMethod`, `illuminaOutlierMethod`

### Examples

    ## Not run:

        if(require(beadarrayExampleData)){

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

    }

    ## End(Not run)

[Package beadarray version 2.44.0 Index]