Background Correction
Background corrects probe intensities in an object of class
AffyBatch.
bg.correct(object, method, ...) bg.correct.rma(object,...) bg.correct.mas(object, griddim) bg.correct.none(object, ...)
object |
An object of class |
method |
A |
griddim |
grid dimension used for mas background estimate. The array is divided into griddim equal parts. Default is 16. |
... |
arguments to pass along to the engine function. |
The name of the method to apply must be double-quoted. Methods provided with the package are currently:
bg.correct.none: returns object unchanged.
bg.correct.chipwide: noise correction as described in a ‘white paper’ from Affymetrix.
bg.correct.rma: the model based correction used by the RMA expression measure.
They are listed in the variable bg.correct.methods. The user must
supply the word after "bg.correct", i.e none, subtractmm, rma, etc...
More details are available in the vignette.
R implementations similar in function to the internal implementation used by
bg.correct.rma are in bg.adjust.
An AffyBatch for which the
intensities have been background adjusted.
For some methods (RMA), only PMs are corrected and the MMs remain the
same.
if (require(affydata)) {
data(Dilution)
##bgc will be the bg corrected version of Dilution
bgc <- bg.correct(Dilution, method="rma")
##This plot shows the tranformation
plot(pm(Dilution)[,1],pm(bgc)[,1],log="xy",
main="PMs before and after background correction")
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