HULK {beadarray} | R Documentation |
Normalizes an probe intensities by calculating a weighted average residual based on the residuals of the surrounding probes.
HULK(BLData, array, neighbours = NULL, invasions = 20, what = "G")
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. |
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.
An object of class BeadLevelList
Mike Smith
Cairns JM, Dunning MJ, Ritchie ME, Russell R, Lynch AG. (2008). BASH: a tool for managing BeadArray spatial artefacts. Bioinformatics, 24(24):2921-2.
data(BLData) o <- HULK(BLData, 1)