PM Correction
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 |
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)
}Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.