extEAWP: extract basic data from expression data objects
In geantonicelli/GLM: set of wrapper and adapter functions for statistical analysis

Description Usage Arguments Details Value Author(s) See Also

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 the limma package or by limmaDE() in the GLM package

1	extEAWP(object)

object

any matrix-like object containing log-expression values, it 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

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

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

gerardo esteban antonicelli

'check_contrasts' 'omega_factorial'

geantonicelli/GLM documentation built on Dec. 15, 2020, 3:05 p.m.