compute.affinities: Probe Affinity computation
In gcrma: Background Adjustment Using Sequence Information

Description Usage Arguments Details Value Author(s) References See Also

An internal function to calculate probe affinities from their sequences.

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compute.affinities(cdfname,verbose=TRUE)
compute.affinities2(cdfname,verbose=TRUE)
check.probes(probepackage,cdfname)

`cdfname`	Object of class `character` representing the name of `CDF` file associated with the arrays in the `AffyBatch`.
`probepackage`	`character` representing the name of the package with the probe sequence information.
`verbose`	Logical value. If `TRUE` messages about the progress of the function is printed.

The affinity of a probe is described as the sum of position-dependent base affinities. Each base at each position contributes to the total affinity of a probe in an additive fashion. For a given type of base, the positional effect is modeled as a spline function with 5 degrees of freedom.

Use compute.affinities2 if there are no MM probes.

check.probes makes sure things are matching as they should.

compute.affinities returns an AffyBatch with the affinities for PM probes in the pm locations and the affinities for MM probes in the mm locations. NA will be added for probes with no sequence information.

Rafeal Irizarry

Hekstra, D., Taussig, A. R., Magnasco, M., and Naef, F. (2003) Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide array. Nucleic Acids Research, 31. 1962-1968.

gcrma,affinity.spline.coefs

gcrma documentation built on Nov. 8, 2020, 5:12 p.m.