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 `merge`. 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 1.48.0 Index]