getEAWP: Extract Basic Data from Microarray Data Objects

In richierocks/limma2: Linear Models for Microarray Data

Description

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

Usage

getEAWP(object)

Arguments

object

a microarray data object. An object of class list, MAList, EList, marrayNorm, PLMset, vsn, or any class inheriting from ExpressionSet, or any object that can be coerced to a numeric matrix.

Details

In the case of two-color objects, the Amean is computed from the matrix of A-values. For single-channel objects, Amean is computed from the matrix of expression vales. PLMset, vsn and ExpressionSet are assumed to be single-channel for this purpose.

If object is a matrix, it is assumed to contain log-intensities if the values are all positive and log-ratios otherwise. Amean is computed in the former case but not the latter.

From April 2013, the output exprs matrix is ensured to have unique row names. If object has no row names, then the output row names of exprs are 1 to the number of rows. If object has row names but with duplicated names, then row names of exprs are set to 1 up to the number of rows and the original row names are preserved in the ID column of probes.

Value

A list with components

exprs	numeric matrix of log-ratios or log-intensities
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.

richierocks/limma2 documentation built on May 27, 2019, 8:47 a.m.