affy: normalize.contrast – R documentation

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affy

normalize.contrast

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.