normScaleLimma: Scale adjust a cDNA Microarray Object

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

Description

This function loads a maigesRaw or maiges object and scale adjust (normalise between arrays) the data using functions from limma package.

Usage

normScaleLimma(obj=NULL, ...)

Arguments

obj	object of type maigesRaw or maiges to be normalised.
...	additional parameters for function normalizeBetweenArrays.

Details

This function for scale adjustment is entirely based on function normalizeBetweenArrays from limma package. See the help page for this function to see how to set the parameters. Pay attention to the 'vsn' method of scale adjustment, that must be used alone.

Value

This function returns a maiges object.

Author(s)

Gustavo H. Esteves <[e-mail]>

See Also

normalizeBetweenArrays from limma package.

Examples

## Loading the dataset
data(gastro)

## Doing the scale adjustment from median-absolute-value method (from
## limma)
gastro.norm = normScaleLimma(gastro.norm, method="scale")
boxplot(gastro.norm) ## To see the efect of adjustment

## To do VSN scale adjustment (from vsn package) use the command. Be
## carefull that this method adjust the variance along A values and not
## between chips!!
gastro.norm = normScaleLimma(gastro.raw2, method="vsn")
boxplot(gastro.norm) ## See the effect

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