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]