getEAWP {limma} | R Documentation

## Extract Basic Data from Expression Data Objects

### Description

Given an expression data object of any known class, get the expression values, weights, probe annotation and A-values that are needed for linear modelling. This function is called by the linear modelling functions in LIMMA.

### Usage

    getEAWP(object)

### Arguments

`object` | any matrix-like object containing log-expression values. Can be an object of class `MAList`, `EList`, `marrayNorm`, `PLMset`, `vsn`, or any class inheriting from `ExpressionSet`, or any object that can be coerced to a numeric matrix.

### Details

Rows correspond to probes and columns to RNA samples.

In the case of two-color microarray data objects (`MAList` or `marrayNorm`), `Amean` is the vector of row means of the matrix of A-values. For other data objects, `Amean` is the vector of row means of the matrix of expression values.

From April 2013, the rownames of the output `exprs` matrix are required to be unique. If `object` has no row names, then the output rownames of `exprs` are `1:nrow(object)`. If `object` has row names but with duplicated names, then the rownames of `exprs` are set to `1:nrow(object)` and the original row names are preserved in the `ID` column of `probes`.

`object` should be a normalized data object. `getEAWP` will return an error if `object` is a non-normalized data object such as `RGList` or `EListRaw`, because these do not contain log-expression values.

### Value

A list with components

`exprs` | numeric matrix of log-ratios, log-intensities or log-expression values
`weights` | numeric matrix of weights
`probes` | data.frame of probe-annotation
`Amean` | numeric vector of average log-expression for each probe

`exprs` is the only required component. The other components will be `NULL` if not found in the input object.

### Author(s)

Gordon Smyth

### See Also

02.Classes gives an overview of data classes used in LIMMA.

[Package limma version 3.42.2 Index]