RGList_CALIB-class {CALIB} | R Documentation

## Red, Green Intensity List - Class

### Description

A simple list-based class for storing red and green channel foreground and background intensities for a batch of spotted microarrays. It is a extension of the RGList in the LIMMA package.

### Objects from the Class

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

### List Components

objects should contain the following list components:

`R`:
  numeric matrix containing the red(Cy5) foreground intensities. Rows correspond to spots and columns to arrays.
`G`:
  numeric matrix containing the green(Cy3) foreground intensities.
`Rb`:
  numeric matrix containing the red(Cy5) background intensities.
`Gb`:
  numeric matrix containing the green(Cy3) background intensities.
`RArea`:
  numeric matrix containing the red(Cy5) spot areas.
`GArea`:
  numeric matrix containing the green(Cy3) spot areas.

Optional components include:

`weights`:
  numeric matrix containing relative spot quality weights. Should be non-negative.
`printer`:
  list containing information on the process used to print the spots on the arrays. See `read.rg`.
`genes`:
  data.frame containing information on the genes spotted on the arrays. Should include a character column Name containing names for the genes or controls.
`targets`:
  data.frame containing information on the target RNA samples. Should include factor or character columns Cy3 and Cy5 specifying which RNA was hybridized to each array.
`other`:
  list containing numeric matrices of other spot-specific information.

All of the matrices should have the same dimensions. The row dimension of targets should match the column dimension of the matrices.

### Extends

Class `"list"`, from data part. Class `"LargeDataObject"`, directly. 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, RGList_CALIB objects can be `subsetted`, `combined` and `merged`. RGList_CALIB objects will return dimensions and hence functions such as `dim`, `dimnames`, `nrow` and `ncol` are defined. RGList_CALIB also inherit a `show` method from the virtual class `LagerDataObject`, which means that RGList_CALIB objects will print in a compact way.

In the CALIB package, RGList_CALIB objects are mainly for storing microarray data and they are used to pass microarray data into functions such as `estimateParameter` or `normalizeData`.

### Author(s)

Hui Zhao

### References

`RGList` in the limma package

### See Also

`RGList` and `LargeDataObject` in limma packge.

[Package CALIB version 1.6.0 Index]