rmaplus: Derive RMA+ intensities

Description Usage Arguments Value Author(s) References See Also Examples

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

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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([email protected])

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

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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 May 2, 2018, 4:28 a.m.