Description Objects from the Class List Components Extends Methods Author(s) References

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

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`

.

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.

Class `"list"`

, from data part.
Class `"vector"`

, by class `"list"`

.

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.

Hui Zhao

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

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