| rmaplus {RefPlus} | R Documentation |
Calculate the RMA+ intensities using pre-stored reference quantiles and probe effects. The reference quantiles and the probe effects are the estimated parameter values from RMAing a set of microarrays (e.g. a reference set).
rmaplus(Future, rmapara, r.q, p.e, bg = TRUE)
Future |
An affybatch object of the microarrays to be
pre-processed using the RMA+ methods. |
rmapara |
Output of rma.para function that the contain reference
quantiles and the reference probe effects. |
r.q |
The pre-stored vector of the quantiles that the probe intensity data of a microarray should be normalized to. |
p.e |
A pre-stored list of probe effects. It is a probe.coefs object of
PLMset class in affyPLM package. |
bg |
A logical flag. If True(by default), background correct
Train using default bg.correct.rma. |
The RMA+ intensities of Future.
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.
PLMset-class,rma.para,
rmaref.predict
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)
}