threestepPLM {affyPLM}R Documentation

Three Step expression measures returned as a PLMset

Description

This function converts an AffyBatch into an PLMset using a three step expression measure.

Usage

threestepPLM(object,subset=NULL, normalize=TRUE,background=TRUE,background.method="RMA.2",normalize.method="quantile",summary.method="median.polish",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.
summary.method name of summary method to use.
background.param list of parameters for background correction methods
normalize.param list of parameters for normalization methods
output.param list of parameters for output methods
model.param list of parameters for model methods

Details

This function computes the expression measure using threestep methods. It returns a PLMset. The most important difference is that the PLMset allows you to access the residuals which the threestep function does not do.

Value

An PLMset

Author(s)

Ben Bolstad bolstad@stat.berkeley.edu

References

Bolstad, BM (2004) Low Level Analysis of High-density Oligonucleotide Array Data: Background, Normalization and Summarization. PhD Dissertation. University of California, Berkeley.

See Also

expresso, rma, threestep, rmaPLM, fitPLM

Examples

data(affybatch.example)

# should be equivalent to rma()
## Not run: eset <- threestepPLM(affybatch.example)

[Package affyPLM version 1.6.0 Index]