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.