RefPlus-package {RefPlus}R Documentation

RMA based on reference microarrays: RMA+ and RMA++ methods

Description

RMA+ is an extenstion of the RMA algorithm that calculates the probeset intensities of a microarray using a pre-stored RMA model fitted on previously obtained microarrays, e.g. reference microarrays. RMA++ is a further extension based on the RMA+ method. This package depends on the affyPLM package.

Details

Package: RefPlus
Type: Package
Version: 1.2.0
Date: 2006-10-25
License: GPL version 2 or newer

Use rma.para to obtain the reference quantiles and the probe effects from a reference set, then use rmaplus to calculate the RMA+ intensities based on the fitted reference quantiles and probe effects.

Author(s)

By Kai-Ming Chang(Kai-Ming.Chang@astrazeneca.com, kaiming@gmail.com)

References

Chang,K.M., Harbron,C., South,M.C. (2006) An Exploration of Extensions to the RMA Algorithm. (Submitted)

Examples

## Use affybatch.example in affy package
data(affybatch.example)

##Calculate RMA intensities using the rma function.
Ex0<-exprs(rma(affybatch.example))

## Background correct, estimate the probe effects, and calculate the 
## RMA intensities using rma.para function.
Para<-rma.para(affybatch.example,bg=TRUE,exp=TRUE)
Ex1<-Para[[3]]
 
## Calculate the RMA+ intensity using rmaplus function. 
Ex2<-rmaplus(affybatch.example, rmapara=Para, bg = TRUE)


[Package RefPlus version 1.4.0 Index]