BASHExtended {beadarray} | R Documentation

## BASH - Extended Defect Analysis

### Description

Returns a score, which assesses the extent to which the background is changing across the array/strip.

### Usage

    BASHExtended(BLData, array, neighbours = NULL, E = NULL, E.BG = NULL)

### Arguments

`BLData` | `BeadLevelList`
`array` | integer specifying which strip/array to plot
`neighbours` | A Neighbours matrix. Optional - if left NULL, it will be computed, using default `generateNeighbours` settings.
`E` | Numerical vector - The error image to use. Optional - if left blank, it will be computed, using `generateE` (with `bgfilter = "none"`, i.e. no background filter applied).
`E.BG` | Numerical vector - The background error image to use. Optional - if left blank, it will be computed from `E`, using default `BGFilter` settings (i.e. `method = "median"`).

### Details

`BASHExtended` assesses the change of background across an array.

The error image used should not be background filtered (as opposed to the error image used in `BASHDiffuse`). Here, E is the error image

### Value

Scalar (Extended defect score)

### Author(s)

Jonathan Cairns

### References

Mayte Suarez-Farinas, Maurizio Pellegrino, Knut M. Wittkwosky and Marcelo O. Magnasco (2007). Harshlight: A "corrective make-up" program for microarray chips. R package version 1.8.0. http://asterion.rockefeller.edu/Harshlight/

### See Also

`BASH`, `generateE`, `BGFilter`, `generateNeighbours`,

### Examples

    data(BLData)
    an <- arrayNames(BLData)
    extended <- NULL

    for(i in 1:length(an))
    {
            extended[i] <- BASHExtended(BLData, i)
    }

[Package beadarray version 1.12.1 Index]