RefPlus (version 1.42.0)

RefPlus-package: 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:

1.13.2

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.

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)
}