normScaleMarray: Scale adjust a cDNA Microarray Object

Description

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

Usage

normScaleMarray(obj=NULL, ...)

Arguments

obj

object of type maigesRaw or maiges to be normalised.

...

additional parameters for function maNormScale.

Value

This function returns a maiges object.

Details

This function for scale adjustment is entirely based on function maNormScale from marray package. See the help page for this function to see how to set the parameter. Pay attention to the subset argument that is fixed directly from the UseSpots and BadSpots from obj object, and must not be specified in the additional arguments.

The functionality of the scale adjustment function from marray package was added because it uses an estimator of MAD different from that one used in limma package. Also, using maNormScale function it is possible to do print tip scale adjustment.

Examples

Run this code

## Loading the dataset
data(gastro)

## Doing global MAD scale adjustment
gastro.norm = normScaleMarray(gastro.norm, norm="globalMAD")
boxplot(gastro.norm) ## To see the effect of MAD adjustment

## For print tip MAD use the following command
## Not run: 
# gastro.norm = normScaleMarray(gastro.norm, norm="printTipMAD")
# ## End(Not run)