R: Extract Basic Data from Expression Data Objects

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