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 components:

`M`: | numeric matrix containing the M-values (log-2 expression ratios). Rows correspond to spots and columns to arrays.
`A`: | numeric matrix containing the A-values (average log-2 expression values).

Optional components include:

`weights`: | numeric matrix of same dimensions as `M` containing relative spot quality weights. Elements should be non-negative.
`other`: | list containing other matrices, all of the same dimensions as `M`.
`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 `MAList` 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, `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` is the corresponding class in the marray package.

[Package limma version 3.42.2 Index]