rmaPLM {affyPLM} | R Documentation

## Fit a RMA to Affymetrix Genechip Data as a PLMset

### Description

This function converts an `AffyBatch` into an `PLMset` by fitting a multichip model. In particular we concentrate on the RMA model.

### Usage

    rmaPLM(object,subset=NULL,normalize=TRUE,background=TRUE,background.method="RMA.2",normalize.method="quantile",background.param = list(),normalize.param=list(),output.param=list(),model.param=list())

### Arguments

`object` | an `AffyBatch`
`subset` | a vector with the names of probesets to be used. If NULL then all probesets are used.
`normalize` | logical value. If `TRUE` normalize data using quantile normalization
`background` | logical value. If `TRUE` background correct using RMA background correction
`background.method` | name of background method to use.
`normalize.method` | name of normalization method to use.
`background.param` | A list of parameters for background routines
`normalize.param` | A list of parameters for normalization routines
`output.param` | A list of parameters controlling optional output from the routine.
`model.param` | A list of parameters controlling model procedure

### Details

This function fits the RMA as a Probe Level Linear models to all the probesets in an `AffyBatch`.

### Value

An `PLMset`

### Author(s)

Ben Bolstad bolstad@stat.berkeley.edu

### References

Under Preparation

### See Also

`expresso`, `rma`, `threestep`,`fitPLM`, `threestepPLM`

### Examples

    # A larger example testing weight image function
    data(Dilution)
    Pset <- rmaPLM(Dilution,output.param=list(weights=TRUE))
    image(Pset)

[Package affyPLM version 1.2.7 Index]