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: | 1.4.0
Date: | 2007-08-16
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(kaiming@mail.kfcc.org.tw)

### References

Chang,K.M., Harbron,C., South,M.C. (2006) An Exploration of Extensions to the RMA Algorithm. Available with the RefPlus package.

Harbron, C, Chang, K.M., South,M.C.(2007) RefPlus : an R package extending the RMA Algorithm. Bioinformatics 2007; doi: 10.1093/bioinformatics/btm357

### 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 1.8.1 Index]