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

02.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 2.4.7 Index]