aroma.affymetrix (version 2.11.1)

fit.SingleArrayUnitModel: Estimates the model parameters

Description

Estimates the model parameters for all or a subset of the units.

Usage

## S3 method for class 'SingleArrayUnitModel':
fit(this, arrays=NULL, units="remaining", ..., force=FALSE, verbose=FALSE)

Arguments

arrays

The arrays to be fitted. If NULL, all arrays are considered. If remaining, only non-fitted arrays are considered.

units

The units to be fitted. If NULL, all units are considered. If remaining, only non-fitted units are considered.

...

Arguments passed to *readUnits().

force

If TRUE, already fitted units are re-fitted, and cached data is re-read.

verbose

See Verbose.

Value

• Returns nothing.

Details

All estimates are stored to file.

The parameter estimates specific to each array, typically "chip effects", are stored in array specific files.

Array-specific estimates [K = nbr of arrays]: theta [K doubles] (chip effects), sd(theta) [K doubles], isOutlier(theta) [K logicals]

For each array and each unit group, we store: 1 theta, 1 sd(theta), 1 isOutlier(theta), i.e. (float, float, bit) => For each array and each unit (with $G_j$ groups), we store: $G_j$ theta, $G_j$ sd(theta), $G_j$ isOutlier(theta), i.e. $G_j$*(float, float, bit).

See Also

For more information see SingleArrayUnitModel.