codelink (version 1.40.2)

normalize: Normalization wrapper for Codelink/CodelinkSet objects.

Description

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

Usage

"normalize"(object, method="quantiles", log.it=TRUE, preserve=FALSE, weights=NULL, loess.method="fast")
	
"normalize"(object, method="quantile", log.it=TRUE, weights=NULL, loess.method="fast") 
"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'.

Value

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.

Examples

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