SpikeList-class {CALIB} | R Documentation

## Class "SpikeList" - Spike Intensity and Concentration List

### Description

A simple list-based class for storing red and green channel foreground and background intensities, spot area and concentrations for external control spike on spotted microarray.

### Objects from the Class

Objects can be created by calls of the form `new("SpikeList", spike)` where spike is a list. In the CALIB package, SpikeList objects are normally generated by function `read.spike`.

### List Components

Objects should contain the following list components:

`R`:
  numeric matrix containing the red(Cy5) foreground intensities of all external control spikes on arrays. Rows correspond to spikes and columns to arrays.
`G`:
  numeric matrix containing the green(Cy3) foreground intensities of all external control spikes on arrays.
`Rb`:
  numeric matrix containing the red(Cy5) background intensities of all external control spikes on arrays.
`Gb`:
  numeric matrix containing the green(Cy3) background intensities of all external control spikes on arrays.
`RArea`:
  numeric matrix containing the red(Cy5) spot areas of all external control spikes on arrays.
`GArea`:
  numeric matrix containing the green(Cy3) spot areas of all external control spikes on arrays.
`RConc`:
  numeric matrix containing the red(Cy5) known concentrations of all external control spikes on arrays.
`GConc`:
  numeric matrix containing the green(Cy3) know concentrations of all external control spikes on arrays.
`genes`:
  data.frame containing information on spikes spotted on the arrays. Should include a character column Name containing names for all the spikes.

All of the matrices should have the same dimensions.

### Extends

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

### Methods

This class inherits directly from class List, so any operation appropriate for lists will work on objects of this class. In addition, SpikeList objects can be `subsetted`, `combined` and `merged`. SpikeList objects will return dimensions and hence functions such as `dim`, `dimnames`, `nrow` and `ncol` are defined. Generic method `show` is applied on `SpikeList`, so SpikeList will print in a compact way.

SpikeList objects are used on functions such as `estimateParameter` or on some other data visualization functions like `plotSpikeHI` in the CALIB package.

### Author(s)

Hui Zhao

### References

the limma package

### See Also

`RGList_CALIB`.

`RGList` in limma package.

[Package CALIB version 1.4.0 Index]