rmaplus: Derive RMA+ intensities

In RefPlus: A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.

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([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.

See Also

PLMset-class,rma.para, rmaref.predict

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.