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 2.2.0 Index]