| backgroundCorrect2 {OLIN} | R Documentation |
Background correction based on
backgroundCorrect of the limma package.
backgroundCorrect2(object,method="subtract", offset=0)
object |
object of class |
method |
method for background correction: “none”, “subtract”, “half”, “minimum”, “movingmin”, “edwards” or “normexp”. |
offset |
numeric value to add to intensities |
This function is a wrapper function for
backgroundCorrect
with following methods implemented:
“none”: no background correction
“subtract”: simple subtraction of background intensities
“movingmin”: background intensities are first averaged over 3x3 grids of neighbouring spots and subsequently substracted
“minimum”: zero or negative intensities after background correction are set equal to half the minimum of positive corrected intensities
“edwards”: background correction based on log-linear interpolation
“normexp”: background correction based on fitting procedure
For further details and references, please refer to its help page. An
alternative Bayesian model for background correction
(kooperberg) is also implemented
in the limma package.
Background correct object of class marrayRaw.
Matthias Futschik
# Loading data data(sw) #No background correction sw.none <- backgroundCorrect2(sw,method="none") plot(maA(sw.none)[,1],maM(sw.none)[,1]) # Simple subtraction sw.sub <- backgroundCorrect2(sw,method="sub") points(maA(sw.sub)[,1],maM(sw.sub)[,1],col="red")