affy (version 1.50.0)

find.params.pdnn: A function to find the experiment specific PDNN parameters

Description

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

Usage

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

Arguments

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

Value

• A list of
• lambda
  The lambda's
• Bs
  The B's
• Ns
  The N's
• Fs
  The F's

Details

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...

References

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

Examples

## 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)