| getEAWP {limma} | R Documentation |
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.
getEAWP(object)
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. |
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.
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 |
Gordon Smyth
02.Classes gives an overview of data classes used in LIMMA.