pmcorrect {affy} | R Documentation |
Corrects the PM intensities in a ProbeSet
for nonspecific binding.
pmcorrect.pmonly(object) pmcorrect.subtractmm(object) pmcorrect.mas(object, contrast.tau=0.03, scale.tau=10, delta=2.0e-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 detla 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.
A ProbeSet
for which the pm
slot contains the
corrected
PM values.
Affymetrix MAS 4.0 and 5.0 manual
data(affybatch.example) gn <- geneNames(affybatch.example) pps <- probeset(affybatch.example, gn[1])[[1]] pps.pmonly <- pmcorrect.pmonly(pps) pps.subtractmm <- pmcorrect.subtractmm(pps) pps.mas5 <- pmcorrect.mas(pps) par(mfrow=c(2,2)) #plot(pm(pps.pmonly), pm(pps.subtractmm)) #plot(pm(pps.pmonly),pm(pps.mas5)) #plot(pm(pps.subtractmm),pm(pps.mas5))