Description Usage Arguments Details Value Author(s) See Also
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.
1 | getEAWP(object)
|
object |
a microarray data object.
An object of class |
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
.
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.
Gordon Smyth
02.Classes gives an overview of data classes used in LIMMA.
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