rmaplus {RefPlus}R Documentation

Derive RMA+ intensities

Description

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).

Usage

rmaplus(Future, rmapara, r.q, p.e, bg = TRUE)

Arguments

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.

Value

The RMA+ intensities of Future.

Author(s)

Kai-Ming Chang(Kai-Ming.Chang@astrazeneca.com, kaiming@gmail.com)

References

Chang,K.M., Harbron,C., South,M.C. (2006) An Exploration of Extensions to the RMA Algorithm. (Submitted)

See Also

PLMset-class,rma.para, rmaref.predict

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 1.4.0 Index]