pmcorrect: PM Correction
In affy: Methods for Affymetrix Oligonucleotide Arrays

Description Usage Arguments Details Value References Examples

Corrects the PM intensities in a ProbeSet for non-specific binding.

pmcorrect.pmonly(object)

pmcorrect.subtractmm(object)

pmcorrect.mas(object, contrast.tau=0.03, scale.tau=10, delta=2^(-20))

`object`	An object of class `ProbeSet`.
`contrast.tau`	a number denoting the contrast tau parameter in the MAS 5.0 pm correction algorithm.
`scale.tau`	a number denoting the scale tau parameter in the MAS 5.0 pm correction algorithm.
`delta`	a number denoting the delta parameter in the MAS 5.0 pm correction algorithm.

These are the pm correction methods perfromed by Affymetrix MAS 4.0 (subtractmm) and MAS 5.0 (mas). See the Affymetrix Manual for details. pmonly does what you think: does not change the PM values.

A ProbeSet for which the pm slot contains the corrected PM values.

Affymetrix MAS 4.0 and 5.0 manual

if (require(affydata)) {
  data(Dilution)
  gn <- geneNames(Dilution)
  pps <- probeset(Dilution, gn[1])[[1]]

  pps.pmonly <- pmcorrect.pmonly(pps)
  pps.subtractmm <- pmcorrect.subtractmm(pps)
  pps.mas5 <- pmcorrect.mas(pps)
}