find.params.pdnn: A function to find the experiment specific PDNN parameters
In affypdnn: Probe Dependent Nearest Neighbours (PDNN) for the affy package

Description Usage Arguments Details Value References See Also Examples

View source: R/find.params.pdnn.R

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

1	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

pdnn.params.chiptype, generateExprVal.method.pdnn

## load a chip-specific parameter file
## (as returned by the function pdnn.params.chiptype)
data(hgu95av2.pdnn.params)

## load experimental data
library(affydata)
data(Dilution)

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