find.params.pdnn {affypdnn}R Documentation

A function to find the experiment specific PDNN parameters


A function to find the paramaters specific to the chips in an AffyBatch object.


find.params.pdnn(abatch, params.chiptype, optim.method = "BFGS", verbose = TRUE, give.warnings=TRUE)


abatch an instance of Affybatch-class.
params.chiptype chip-type specific parameters (see details)
optim.method method for the optimization function optim. When FALSE, a steepest-descent method of our own is used.
verbose verbosity (TRUE or FALSE)
give.warnings report probeset IDs in the abatch that could not be found in the params.chiptype


This function fits PDNN parameters that are specific to experimental values. The parameters common to all the chips of a certain type are returned by the function pdnn.params.chiptype. If NULL, the parameter files included in the package will be used whenever possible...


A list of

lambda The lambda's
Bs The B's
Ns The N's
Fs The F's


Li Zhang, Michael F. Miles and Kenneth D. Aldape - A model of molecular interactions on short oligonucleotide arrays, 2003, Nature Biotech., vol. 21, n.7

See Also

pdnn.params.chiptype, generateExprVal.method.pdnn


## load a chip-specific parameter file
## (as returned by the function pdnn.params.chiptype)

## load experimental data

## one CEL to go faster
afbatch <- Dilution[, 1]
params <- find.params.pdnn(afbatch, hgu95av2.pdnn.params, optim.method =
FALSE, give.warnings=FALSE)

[Package affypdnn version 1.1-0 Index]