generateExprVal.method.farms {farms}R Documentation

Generate an expression value from the probes informations

Description

Generate an expression from the probe

Usage

          generateExprVal.method.farms(probes, weight, mu, scale, cyc, tol, ...)
          

Arguments

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

Value

A list containing entries:

exprs The expression values.
se.exprs Estimate of the hidden variable.

See Also

generateExprSet-methods,generateExprVal.method.playerout,li.wong, medianpolish

Examples

  data(SpikeIn) ##SpikeIn is a ProbeSets
  probes <- pm(SpikeIn)
  exprs.farms <- generateExprVal.method.farms(probes)

[Package farms version 1.2.2 Index]