normalize {codelink}R Documentation

Normalization wrapper for Codelink objects.

Description

Takes a Codelink object and applies normalization to intensity values.

Usage

    normalize(object, method = "quantiles", log.it = TRUE, preserve = FALSE,
                weights = NULL, verbose = FALSE)

Arguments

object an object of class "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 vector for method CyclicLoess.
verbose should informative output be printed.

Details

Currently supported methods include "loess", "quantiles" and "median". Median normalization is analogous to the default method applied for the manufacturer in the Codelink software. Loess is a modified version of CyclicLoess implemented in the affy package, allowing missing values and weights. Quantile normalization uses the normalizeQuantiles() function in the limma package.

Value

A Codelink object with normalized intensity values.

Author(s)

Diego Diez

Examples

## Not run: 
        data(codelink.example)
        # Background correction.
        codelink.example <- bkgdCorrect(codelink.example,
        method = "half")
        # Normalization.
        codelink.example <- normalize(codelink.example,
        method = "quantile")
## End(Not run)

[Package codelink version 1.10.0 Index]