normalize: Normalization wrapper for Codelink/CodelinkSet objects.

In codelink: Manipulation of Codelink microarray data

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.
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")

codelink documentation built on Nov. 8, 2020, 8:19 p.m.