EList-class {limma} | R Documentation

## Expression List - class

### Description

Simple list-based classes for storing expression values (E-values) for a set of one-channel microarrays. `EListRaw` holds expression values on the raw scale. `EList` holds expression values on the log scale, usually after background correction and normalization. `EListRaw` objects are normally created by `read.maimages`. In the future, `EList` objects are likely to be created `normalizeBetweenArrays`.

### Slots/List Components

`EList` objects can be created by `new("EList",E)` where `E` is a list. These classes contains no slots (other than `.Data`), but objects should contain a list component `E` as follows:

`E`: | numeric matrix containing the E-values (raw or log-2 expression ratios). Rows correspond to spots and columns to arrays.

Optional components include:

`weights`: | numeric matrix of same dimensions as `E` containing relative spot quality weights. Elements should be non-negative.
`other`: | list containing other matrices, all of the same dimensions as `E`.
`genes`: | data.frame containing probe information. Should have one row for each probe. 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.

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

### Methods

These classes inherit directly from class `list` so any operation appropriate for lists will work on objects of this class. In addition, `EList` objects can be subsetted and combined. `EList` objects will return dimensions and hence functions such as `dim`, `nrow` and `ncol` are defined. `ELists` also inherit a `show` method from the virtual class `LargeDataObject`, which means that `ELists` will print in a compact way.

### Author(s)

Gordon Smyth

### See Also

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

`ExpressionSet-class` is a more formal class in the Biobase package.

[Package limma version 2.18.3 Index]