MAList-class {limma}R Documentation

M-value, A-value Expression List - class

Description

A simple list-based class for storing M-values and A-values for a batch of spotted microarrays. MAList objects are usually created during normalization by the functions normalizeWithinArrays or MA.RG.

Slots/List Components

MAList objects can be created by new("MAList",MA) where MA is a list. This class contains no slots (other than .Data), but objects should contain the following list components:
M: numeric matrix containing the M-values or log-2 expression ratios. Rows correspond to spots and columns to arrays.
A: numeric matrix containing the A-values or average log-2 expression values
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.

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, MAList objects can be subsetted and combined. RGList objects will return dimensions and hence functions such as dim, nrow and ncol are defined. MALists also inherit a show method from the virtual class LargeDataObject, which means that RGLists will print in a compact way.

Other functions in LIMMA which operate on MAList objects include normalizeWithinArrays, normalizeBetweenArrays, normalizeForPrintorder, plotMA and plotPrintTipLoess.

Author(s)

Gordon Smyth

See Also

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

marrayNorm-class is the corresponding class in the marrayClasses package.


[Package limma version 2.4.7 Index]