find.params.pdnn {affypdnn} | R Documentation |
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
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)