normLoc: Normalise a cDNA Microarray Object

In maigesPack: Functions to handle cDNA microarray data, including several methods of data analysis

Description

This function loads a maigesRaw object and corrects for location bias.

Usage

normLoc(obj=NULL, ...)

Arguments

obj	object of type maigesRaw to be normalised.
...	additional parameters for function normalizeWithinArrays from limma package.

Details

This function for normalisation is entirely based on the function normalizeWithinArrays from limma package. See their help page to known how to setup the parameters correctly. The parameters layout and weights, are automatically specified by the object obj and must not be specified.

Value

This function returns a maiges object.

Author(s)

Gustavo H. Esteves <[e-mail]>

See Also

normalizeWithinArrays from limma package.

Examples

## Loading the dataset
data(gastro)

## Do the normalization by loess method and span 0.4
gastro.norm = normLoc(gastro.raw2, span=0.4, method="loess")

## Do the same normalization without background subtraction
gastro.norm = normLoc(gastro.raw2, span=0.4, method="loess", bc.method="none")

maigesPack documentation built on Nov. 8, 2020, 6:23 p.m.