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

In affy: Methods for Affymetrix Oligonucleotide Arrays

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)

affy documentation built on Nov. 8, 2020, 8:18 p.m.