RGList-class {limma} | R Documentation

## Red, Green Intensity List - class

### Description

A list-based S4 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. Rows correspond to spots and columns to arrays.

Optional components include

`Rb` | numeric matrix containing the red (cy5) background intensities
`Gb` | numeric matrix containing the green (cy3) background intensities
`weights` | numeric matrix of same dimension as `R` containing relative spot quality weights. Elements should be non-negative.
`other` | list containing other matrices, all of the same dimensions as `R` and `G`.
`genes` | data.frame containing probe information. Should have one row for each spot. May have any number of columns.
`targets` | data.frame containing information on the target RNA samples. Rows correspond to arrays. May have any number of columns. Usually includes columns `Cy3` and `Cy5` specifying which RNA was hybridized to each array.
`printer` | list containing information on the process used to print the spots on the arrays. See PrintLayout.

Valid `RGList` objects may contain other optional components, but all probe or array information should be contained in the above components.

### 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

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

`marrayRaw` is the corresponding class in the marray package.

[Package limma version 3.43.8 Index]