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(kaiming@mail.kfcc.org.tw)

### 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

    ## 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 1.8.1 Index]