generateExprVal.method.avgdiff: Generate an expression value from the probes informations

In Bioconductor/affy: Methods for Affymetrix Oligonucleotide Arrays

Generate an expression value from the probes informations

Description

Generate an expression from the probes

Usage

generateExprVal.method.avgdiff(probes, ...)
generateExprVal.method.medianpolish(probes, ...)
generateExprVal.method.liwong(probes, ...)
generateExprVal.method.mas(probes, ...)

Arguments

probes	a matrix of probe intensities with rows representing probes and columns representing samples. Usually pm(probeset) where probeset is a of class ProbeSet.
...	extra arguments to pass to the respective function.

Value

A list containing entries:

exprs	The expression values.
se.exprs	The standard error estimate.

See Also

generateExprSet-methods, generateExprVal.method.playerout, fit.li.wong

Examples

  data(SpikeIn) ##SpikeIn is a ProbeSets
  probes <- pm(SpikeIn) 
  avgdiff <- generateExprVal.method.avgdiff(probes)
  medianpolish <- generateExprVal.method.medianpolish(probes)
  liwong <- generateExprVal.method.liwong(probes)
  playerout <- generateExprVal.method.playerout(probes)
  mas <- generateExprVal.method.mas(probes)
  
  concentrations <- as.numeric(sampleNames(SpikeIn))
  plot(concentrations,avgdiff$exprs,log="xy",ylim=c(50,10000),pch="a",type="b")
  points(concentrations,2^medianpolish$exprs,pch="m",col=2,type="b",lty=2)
  points(concentrations,liwong$exprs,pch="l",col=3,type="b",lty=3)
  points(concentrations,playerout$exprs,pch="p",col=4,type="b",lty=4)
  points(concentrations,mas$exprs,pch="p",col=4,type="b",lty=4)

Bioconductor/affy documentation built on July 21, 2023, 5:23 p.m.