generateExprVal.method.farms {farms} | R Documentation |
Generate an expression from the probe
generateExprVal.method.farms(probes, weight, mu, scale, cyc, tol, ...)
probes |
a matrix of probe intesities with rows representing
probes and columns representing
samples. Usually pm(probeset) where probeset is a
of class ProbeSet |
weight |
Hyperparameter value which determines the influence of the prior. |
mu |
Hyperparameter value which allows to quantify different aspects of potential prior knowledge. A value near zero assumes that most genes do not contain a signal, and introduces a bias for loading matrix elements near zero. |
scale |
Value which compensates for the reduction of variance during preprocessing and factor analysis (some of the data variance is explained by the noise). |
cyc |
Value which determinates the maximum numbers of EM-Steps. |
tol |
Value which determinates the termination tolerance. |
... |
extra arguments to pass to the respective function |
A list containing entries:
exprs |
The expression values. |
se.exprs |
Estimate of the hidden variable. |
generateExprSet-methods
,generateExprVal.method.playerout
,li.wong
, medianpolish
data(SpikeIn) ##SpikeIn is a ProbeSets probes <- pm(SpikeIn) exprs.farms <- generateExprVal.method.farms(probes)