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)