compute.affinities {gcrma} | R Documentation |
An internal function to calculate probe affinities from their sequences.
compute.affinities(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.
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.