affy (version 1.50.0)

threestepPLM: 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(), 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

Value

• An PLMset

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.

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()
  eset <- threestepPLM(Dilution)
}