BASHExtended {beadarray} | R Documentation |
Returns a score, which assesses the extent to which the background is changing across the array/strip.
BASHExtended(BLData, array, neighbours = NULL, E = NULL, E.BG = NULL)
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" ). |
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
Scalar (Extended defect score)
Jonathan Cairns
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/
BASH
, generateE
, BGFilter
, generateNeighbours
,
data(BLData) an <- arrayNames(BLData) extended <- NULL for(i in 1:length(an)) { extended[i] <- BASHExtended(BLData, i) }