pmcorrect {affy} | R Documentation

## PM Correction

### Description

Corrects the PM intensities in a `ProbeSet` for nonspecific binding.

### Usage

    pmcorrect.pmonly(object)

    pmcorrect.subtractmm(object)

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

### Arguments

`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.

### Details

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.

### Value

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

### References

Affymetrix MAS 4.0 and 5.0 manual

### Examples

    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))

[Package affy version 1.14.2 Index]