EList-class {limma} | R Documentation

## Expression List (EList) class

### Description

A list-based S4 classes for storing expression values (E-values), for example for a set of one-channel microarrays or a set of RNA-seq samples. `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 often created by `read.maimages`, while `EList` objects are often created by `normalizeBetweenArrays` or by `voom`. Alternatively, an `EList` object can be created directly by `new("EList",x)`, where `x` is a list.

### Required Components

These classes contains no slots (other than `.Data`), but objects should contain a list component `E`:

`E`

  numeric matrix containing expression values. In an `EListRaw` object, the expression values are unlogged, while in an `EList` object, they are log2 values. Rows correspond to probes and columns to samples.

### Optional Components

Optional components include:

`Eb`

  numeric matrix containing unlogged background expression values, of same dimensions as `E`. For an `EListRaw` object only.

`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 samples. May have any number of columns.

Valid `EList` or `EListRaw` objects may contain other optional components, but all probe or sample 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. `EList`s 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` is a more formal class in the Biobase package used for the same purpose.

### Examples

    # Two ways to make an EList object:

    y <- matrix(rnorm(10,5),10,5)
    rownames(y) <- paste0("Gene",1:10)
    colnames(y) <- LETTERS[1:5]
    Genes <- data.frame(Chr=sample(1:21,10))
    row.names(Genes) <- row.names(y)

    # Create the object, than add components:
    E <- new("EList")
    E$E <- y
    E$genes <- Genes

    # Create with components:
    E <- new("EList", list(E=y, genes=Genes))

[Package limma version 3.44.3 Index]