threestepPLM: Three Step expression measures returned as a PLMset

In affyPLM: Methods for fitting probe-level models

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(), verbosity.level=0)

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
verbosity.level	An integer specifying how much to print out. Higher values indicate more verbose. A value of 0 will print nothing

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 [e-mail]

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

if (require(affydata)) {
  data(Dilution)

  # should be equivalent to rma()
  ## Not run: eset <- threestepPLM(Dilution)
}

affyPLM documentation built on Nov. 8, 2020, 6:53 p.m.