calcA: Method calcA to calculate A values

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

Description

Generic function calcA to calculate A values from classes of microarray data objects defined in this package.

Usage

calcA(object, ...)

## Default S3 method:
calcA(object, ...)

## S3 method for class 'maigesRaw'
calcA(object, bkgSub="subtract", ...)

Arguments

object	object of any class. But only some methods are defined in this moment.
bkgSub	character string indicating the type of background subtraction. May be 'none', 'subtract', 'half', 'minimum', 'movingmin', 'edwards', 'normexp' or 'rma'. Uses limma and defaults to 'subtract'.
...	additional parameters for calcA method.

Details

This method receive an object (at moment of class maiges, maigesRaw or maigesANOVA) and returns the matrix of A values. For objects of class maigesRaw it uses the function backgroundcorrect from limma package to do background correction before the calculation of A values.

Author(s)

Gustavo H. Esteves <[e-mail]>

See Also

backgroundcorrect in the limma package and calcW.

Examples

## Loading the dataset
data(gastro)

calcA(gastro.raw)
calcA(gastro.norm)

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