Documentation 
Compute Affymetrix probe affinities from their sequences and MM probe intensities
[AffinPM, AffinMM]
= affyprobeaffinities(SequenceMatrix, MMIntensity)
[AffinPM, AffinMM, BaseProf]
= affyprobeaffinities(SequenceMatrix, MMIntensity)
[AffinPM, AffinMM, BaseProf, Stats]
= affyprobeaffinities(SequenceMatrix, MMIntensity)
... = affyprobeaffinities(SequenceMatrix, MMIntensity,
...'ProbeIndices', ProbeIndicesValue, ...)
... = affyprobeaffinities(SequenceMatrix, MMIntensity,
...'Showplot', ShowplotValue, ...)
SequenceMatrix  An Nby25 matrix of sequence information for the perfect match (PM) probes on an Affymetrix^{®} GeneChip^{®} array, where N is the number of probes on the array. Each row corresponds to a probe, and each column corresponds to one of the 25 sequence positions. Nucleotides in the sequences are represented by one of the following integers:
 
MMIntensity  Column vector containing mismatch (MM) probe intensities from a CEL file, generated from a single Affymetrix GeneChip array. Each row corresponds to a probe.
 
ProbeIndicesValue  Column vector containing probe indexing information. Probes within a probe set are numbered 0 through N  1, where N is the number of probes in the probe set.
 
ShowplotValue  Controls the display of a plot showing the affinity values of each of the four bases (A, C, G, and T) for each of the 25 sequence positions, for all probes on the Affymetrix GeneChip array. Choices are true or false (default). 
AffinPM  Column vector of PM probe affinities, computed from their probe sequences and MM probe intensities. 
AffinMM  Column vector of MM probe affinities, computed from their probe sequences and MM probe intensities. 
BaseProf  4by4 matrix containing the four parameters for a polynomial of degree 3, for each base, A, C, G, and T. Each row corresponds to a base, and each column corresponds to a parameter. These values are estimated from the probe sequences and intensities, and represent all probes on an Affymetrix GeneChip array. 
Stats  Row vector containing four statistics in the following order:

[AffinPM, AffinMM] = affyprobeaffinities(SequenceMatrix, MMIntensity) returns a column vector of PM probe affinities and a column vector of MM probe affinities, computed from their probe sequences and MM probe intensities. Each row in AffinPM and AffinMM corresponds to a probe. NaN is returned for probes with no sequence information. Each probe affinity is the sum of positiondependent base affinities. For a given base type, the positional effect is modeled as a polynomial of degree 3.
[AffinPM, AffinMM, BaseProf] = affyprobeaffinities(SequenceMatrix, MMIntensity) also estimates affinity coefficients using multiple linear regression. It returns BaseProf, a 4by4 matrix containing the four parameters for a polynomial of degree 3, for each base, A, C, G, and T. Each row corresponds to a base, and each column corresponds to a parameter. These values are estimated from the probe sequences and intensities, and represent all probes on an Affymetrix GeneChip array.
[AffinPM, AffinMM, BaseProf, Stats] = affyprobeaffinities(SequenceMatrix, MMIntensity) also returns Stats, a row vector containing four statistics in the following order:
Rsquare statistic
F statistic
pvalue
Error variance
... = affyprobeaffinities(SequenceMatrix, MMIntensity, ...'PropertyName', PropertyValue, ...) calls affyprobeaffinities with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:
... = affyprobeaffinities(SequenceMatrix, MMIntensity,
...'ProbeIndices', ProbeIndicesValue, ...) uses
probe indices to normalize the probe intensities with the median of
their probe set intensities.
Tip Use of the ProbeIndices property is recommended only if your MMIntensity data are not from a nonspecific binding experiment. 
... = affyprobeaffinities(SequenceMatrix, MMIntensity, ...'Showplot', ShowplotValue, ...) controls the display of a plot of the probe affinity base profile. Choices are true or false (default).
[1] Naef, F., and Magnasco, M.O. (2003). Solving the Riddle of the Bright Mismatches: Labeling and Effective Binding in Oligonucleotide Arrays. Physical Review E 68, 011906.
[2] Wu, Z., Irizarry, R.A., Gentleman, R., Murillo, F.M. and Spencer, F. (2004). A Model Based Background Adjustment for Oligonucleotide Expression Arrays. Journal of the American Statistical Association 99(468), 909–917.
[3] Best, C.J.M., Gillespie, J.W., Yi, Y., Chandramouli, G.V.R., Perlmutter, M.A., Gathright, Y., Erickson, H.S., Georgevich, L., Tangrea, M.A., Duray, P.H., Gonzalez, S., Velasco, A., Linehan, W.M., Matusik, R.J., Price, D.K., Figg, W.D., EmmertBuck, M.R., and Chuaqui, R.F. (2005). Molecular alterations in primary prostate cancer after androgen ablation therapy. Clinical Cancer Research 11, 6823–6834.
affygcrma  affyprobeseqread  affyread  celintensityread  probelibraryinfo