ParameterList-class {CALIB} | R Documentation

## Class "ParameterList" - List to store all the parameters

### 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.

[Package CALIB version 1.46.0 Index]