RefPlus-package {RefPlus} | R Documentation |
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.
Package: | RefPlus |
Type: | Package |
Version: | 1.9.0 |
Date: | 2007-11-1 |
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.
By Kai-Ming Chang(kaiming@gmail.com)
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.
## 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)