bg.correct {affy} | R Documentation |
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 AffyBatch . |
method |
A character that defines what background
correction method will be used. Available methods are given by
bg.correct.methods . |
griddim |
grid dimension used for mas background estimate. The array is divided into griddm 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: begin{itemize}
object
unchanged.
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.
bg.correct.rma2
gives access to the older background method
that was used by the rma
function in version 1.1
bioconductor releases. For the 1.2 release rma
performs
the same background adjustment as bg.correct.rma
. Unless you
wish to duplicate older results in which case
you should use bg.correct.rma
.
Details on the internal fucntions 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.
data(affybatch.example) ##bgc will be the bg corrected version of affybatch.example bgc <- bg.correct(affybatch.example,method="rma") ##This plot shows the tranformation plot(pm(affybatch.example)[,1],pm(bgc)[,1],log="xy", main="PMs before and after background correction")