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 1.10.0 Index]