04.Background {limma} | R Documentation |
This page deals with background correction methods for two-color microarray data.
Usually one doesn't need to explicitly ask for background correction of the intensities because this is done by default by normalizeWithinArrays
,
which subtracts the background from the foreground intensities before applying the normalization method.
This default background correction method can be over-ridden by using backgroundCorrect
which offers a number of alternative
background correct methods to simple subtraction.
The function backgroundCorrect
is used to correct the RGList
before applying normalizeWithinArrays
.
The movingmin
method of backgroundCorrect
uses utility functions ma3x3.matrix
and ma3x3.spottedarray
.
The normexp
method of backgroundCorrect
uses utility functions normexp.fit
and normexp.signal
.
kooperberg
is a Bayesian background correction tool designed specifically for GenePix data.
kooperberg
is not currently used as the default method for GenePix data because it is computationally intensive.
It requires several additional columns from the GenePix data files which can be read in using read.maimages
and specifying the other.columns
argument.
Gordon Smyth