RefPlus-package: RMA based on reference microarrays: RMA+ and RMA++ methods

In RefPlus: A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (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:	1.13.2
Date:	2009-03-11
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([e-mail])

References

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

Harbron, C, Chang, K.M., South,M.C.(2007) RefPlus : an R package extending the RMA Algorithm. Bioinformatics 23, 2493-2494.

Examples

if (require(affydata)) {
  ## Use Dilution in affydata package
  data(Dilution)

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

  ## Background correct, estimate the probe effects, and calculate the 
  ## RMA intensities using rma.para function.
  Para<-rma.para(Dilution, bg=TRUE,exp=TRUE)
  Ex1<-Para[[3]]

  ## Calculate the RMA+ intensity using rmaplus function. 
  Ex2<-rmaplus(Dilution, rmapara=Para, bg = TRUE)
}

RefPlus documentation built on Nov. 8, 2020, 5:20 p.m.