ParameterList-class: Class "ParameterList" - List to store all the parameters

In CALIB: Calibration model for estimating absolute expression levels from microarray data

Description

A simple list-based class for storing all the model parameters of a batch of microarray.

Objects from the Class

Objects can be created by calls of the form new("ParameterList", parameter) where parameter is a list. In the CALIB package, ParameterList objects are normally generated by function estimateParameter.

List Components

Objects should contain the following list components:

MuS:

Spot parameter. Mean of spot capacity.

Ka:

Hybridization constant.

P1:

Respective slope of the linear dye saturation function. It is different for different dyes.

P2:

Respective intercept of the linear dye saturation function. It is different for different dyes

SigmaA:

Standard deviation of additive error. It is different for different dyes.

SigmaM:

Standard deviation of multiplicative error.

SigmaS:

Spot parameter. Standard deviation of spot capacity.

SpotError:

numeric matrix containing spot error of all external control spikes on arrays

Method:

boolean values indicating the way to calculate the measured intensities. It contains two subfields which are both logical value: BC and Area. BC indicates whether background corrected measured intensities are used. Area indicates whether spot area is used to calculate measured intensities.

ErrorModel:

a character to represent the distribution of spot capacity. "L" means spot capacity follows log normal distribution. "N" means spot capacity follows normal distribution.

genes:

data.frame containing information on spikes spotted on the arrays. Should include a character column Name containing names for all the spikes.

See reference for more detailed explaination for these list components.

Extends

Class "list", from data part. Class "vector", by class "list".

Methods

This class inherits directly from class List. However since it represents the parameters

of the calibration model for arrays, it makes on sense to run functions like dim,

dimnames,or merge on this class.

Therefore, only some operations appropriate for list will work on objects of this class. ParameterList objects can be cbind and show in a compact way.

ParameterList objects are used on functions such as normalizeData or on some other data visualization functions like plotSpikeHI in the CALIB package.

Author(s)

Hui Zhao

References

Engelen, K., Naudts, B., DeMoor, B., Marchal, K. (2006) A calibration method for estimating absolute expression levels from microarray data. Bioinformatics 22: 1251-1258.

CALIB documentation built on Oct. 31, 2019, 3:45 a.m.