RefPlus (version 1.42.0)

rma.para: Fitting a RMA model

Description

Obtain reference quantiles and reference probe effects based on reference set Train, and calculate the gene expression

Usage

rma.para(Train, bg = TRUE, exp = FALSE)

Arguments

Train

An AffyBatch object of the reference set microarrays.

bg

A logical flag. If True(by default), background correct Train using default bg.correct.rma.

exp

A logical flag. If True, calculate the RMA measurements of Train. If False, return 0.

Value

Reference.Quantiles

Reference quantiles derived from Train.

probe.effects

Estimated probe effects derived from Train.

expression

RMA measurements of Train.

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

rmaplus,rmaref.predict

Examples

if (require(affydata)) {
  ## Use Dilution in affydata package
  data(Dilution)

  ## Background correct, estimate the probe effects, and calculate the 
  ## RMA intensities using rma.para function.
  Ex<-rma.para(Dilution, bg=TRUE,exp=TRUE)

  ## Calculate the rma intensities using rma function.
  Ex0<-exprs(rma(Dilution))

  plot(Ex$express[,1],Ex0[,1])
}