Function to use to transform data prior to running BASH.
neighbours
A Neighbours matrix. Optional - if left NULL, it will be computed, using default generateNeighbours settings.
useLocs
Logical value, specifiying whether the .locs file (if present) should be used to determine neighbours.
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
J. M. Cairns, M. J. Dunning, M. E. Ritchie, R. Russell, and A. G. Lynch (2008). BASH: a tool for managing BeadArray spatial artefacts. Bioinformatics 15; 24(24)