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,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
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

express,expresso, rma, threestep

Examples

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

[Package affyPLM version 1.1.6 Index]