RGList-class {limma} | 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. `RGList` objects are normally created by `read.maimages`.

### Slots/List Components

`RGList` objects can be created by `new("RGList",RG)` where `RG` is a list. Objects of this class contains no slots (other than `.Data`), but 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

Optional components include

`weights`: | numeric matric 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 PrintLayout.
`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.

### Methods

This class inherits directly from class `list` so any operation appropriate for lists will work on objects of this class. In addition, `RGList` objects can be subsetted, combined and merged. `RGList` objects will return dimensions and hence functions such as `dim`, `nrow` and `ncol` are defined. `RGLists` also inherit a `show` method from the virtual class `LargeDataObject`, which means that `RGLists` will print in a compact way.

`RGList` objects can be converted to `exprSet2` objects by `as(RG,"exprSet2")`.

Other functions in LIMMA which operate on `RGList` objects include `normalizeBetweenArrays`, `normalizeForPrintorder`, `normalizeWithinArrays`.

### Author(s)

Gordon Smyth

### See Also

2.Classes gives an overview of all the classes defined by this package.

`marrayRaw-class` is the corresponding class in the marrayClasses package.

[Package limma version 1.9.6 Index]