fit.SingleArrayUnitModel: Estimates the model parameters

In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

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.

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).

Value

Returns nothing.

Author(s)

Henrik Bengtsson

See Also

For more information see SingleArrayUnitModel.

aroma.affymetrix documentation built on May 29, 2024, 4:32 a.m.