| normalize-methods {affy} | R Documentation |
Method for normalizing Affymetrix Probe Level Data
normalize.methods(object)
object |
An AffyBatch. |
If object is an
AffyBatch then
normalize(object) returns an
AffyBatch with the intensities
normalized using the methodology specified by
getOption("BioC")$affy$normalize.method. The affy package
default is quantiles.
Other methodologies can be used by specifying them with the
method argument. For example to use the invariant set
methodology described by Li and Wong (2001) one would type:
normalize(object, method="invariantset").
Further arguments passed by ..., apart from method, are
passed along to the
function responsible for the methodology defined by the method
argument.
A character vector of nicknames for the
methodologies available is returned by
normalize.methods(object)), where object
is an AffyBatch, or simply by
typing normalize.AffyBatch.methods. If the nickname of a method
is called "loess", the help page for that
specific methodology can
be accessed by typing ?normalize.loess.
For more on the normalization methodologies currently implemented please refer to the vignette `Custom Processing Methods'.
To add your own normalization procedures please refer to the customMethods vignette.
data(affybatch.example) normalize.methods(affybatch.example)