rma.para {RefPlus}R Documentation

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.

Note

The RMA procedure requires a lot of computer memory.

Author(s)

Kai-Ming Chang(kaiming@gmail.com)

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

## Use affybatch.example in Affy package
data(affybatch.example)

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

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

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

[Package RefPlus version 1.10.0 Index]