normalize.contrasts {affy}R Documentation

Normalize intensities using the contrasts method

Description

Scale chip objects in an AffyBatch-class.

Usage


normalize.AffyBatch.contrasts(abatch,span=2/3, choose.subset=TRUE,
                              subset.size=5000, verbose=TRUE,
                              family="symmetric",
                              type=c("together","pmonly","mmonly","separate"))

Arguments

abatch an AffyBatch-class object.
span parameter to be passed to the function loess.
choose.subset Boolean. Defaults to TRUE
subset.size Integer. Number of probesets to use in each subset.
verbose verbosity flag.
family parameter to be passed to the function loess.
type a string specifying how the normalization should be applied.

Value

An object of the same class as the one passed.

See Also

maffy.normalize


[Package affy version 1.26.1 Index]