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

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

1 | ```
HULK(BLData, array = 1, neighbours = NULL, invasions = 20, useLocs = TRUE, weightName = "wts", transFun = logGreenChannelTransform, outlierFun = illuminaOutlierMethod)
``` |

`BLData` |
An object of 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. |

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`

A vector of corrected intensities.

Mike Smith

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.

`BASH`

, `insertBeadData`

, `logGreenChannelTransform`

, `squeezedVarOutlierMethod`

, `illuminaOutlierMethod`

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