HULKResids {beadarray} | R Documentation

## HULK - Residuals

### Description

Calculates an set of weighted average residuals, one for each probe, based on the residuals of the surrounding probes.

### Usage

    HULKResids(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

HULKResids calculates a weighted average residual for each probe on the specified array of BLData. It makes use of the same neighbourhood calculations as other BASH functions. The average residuals are 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. It is intended that `HULKResids` be called through `HULK`, but it is quite possible to call it as a stand alone function.

### Value

A vector containing an average residual for each bead on the specified array of BLData.

### 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

`HULK`, `BASH`

### Examples

    data(BLData)
    o <- HULKResids(BLData, 1)

[Package beadarray version 1.12.1 Index]