Normalization wrapper for Codelink/CodelinkSet objects.

Description

Takes a CodelinkSet or Codelink object and applies normalization to intensity values.

Usage

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## S4 method for signature 'Codelink'
normalize(object, method="quantiles", log.it=TRUE, preserve=FALSE, weights=NULL, loess.method="fast")
	
## S4 method for signature 'CodelinkSet'
normalize(object, method="quantile", log.it=TRUE, weights=NULL, loess.method="fast")
    
## S4 method for signature 'CodelinkSet'
codNormalize(object, method="quantile", log.it=TRUE, weights=NULL, loess.method="fast")

Arguments

object

an object of class CodelinkSet or Codelink.

...

further arguments passed to the normalization functions.

method

method to use in normalization.

log.it

logical; if data should be log2.

preserve

logical; if Ri slot should be preserved.

weights

weights for method CyclicLoess.

loess.method

loess method to be used, default to 'fast'.

Details

Currently supported methods include "median", "quantile" and "loess". Normalization functions are borrowed from the limma package.

If a matrix of weights is passed for CyclicLoess normalization, a vector is constructed taking the lowest weight for each probe.

Value

A CodelinkSet or Codelink object with normalized intensity values.

Author(s)

Diego Diez

Examples

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	data(codset)
	# Background correction.
	codset <- codCorrect(codset, method = "half")
	# Normalization.
	codset <- normalize(codset, method = "quantile")

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