A generic function to perform background correction.
bg_correct(iden, Data1, genepix_vars, method = "subtract_local")A character indicating the name of the object to be used under Data1
A data frame with sample identifiers merged with micro array data.
A list of specific definitions of the experiment design.
See array_vars.
a description of the background correction to be used.
Possible values are "none","subtract_local",
"subtract_global","movingmin_bg","minimum_half","edwards" or "normexp".
The default is "subtract_local".
A data frame with background corrected data
Background correction
The function implements background correction methods developed
by backgroundCorrect. But the
minimum_half and movingmin_bg uses the block of the protein array as
the grid. If method="movingmin_bg" the minimum
background value within a block is subtracted.
If method="minimum_half" then any intensity which is negative after
background subtraction is reset to be equal to half the
minimum positive value in
a block. If method="movingmin_value" then any intensity which is negative
after background subtraction is reset to the minimum positive value
in a block. For edwards we implement a similar algorithm with
limma::backgroundCorrect(method="edwards") and for 'normexp'
we use the saddle-point approximation to maximum likelihood,
backgroundCorrect for more details.