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,  cyc, tol, weighted.mean, robust, ...)
          

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 in the range of [0,1] which determines the influence of the prior. The default value is 0.5
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. Default value is 0
cyc Value which determinates the maximum numbers of EM-Steps. Default value is set to number of arrays/2
tol Value which determinates the termination tolerance. Convergence threshold is set to 1E-05.
weighted.mean Boolean flag, that indicates wether a weighted mean or a least square fit is used to summarize the loading matrix. The default value is set to TRUE .
robust Boolean flag, that ensures non-constant results. Default value is TRUE.
... 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 1.4.0 Index]