normalize {codelink} | R Documentation

## Normalization wrapper for Codelink/CodelinkSet objects.

### Description

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

### Usage

    ## 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

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

[Package codelink version 1.48.0 Index]