farms (version 1.24.0)

generateExprVal.method.farms: 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, minNoise, correction, laplacian, centering, spuriousCorrelation, ...)

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 30

tol

Value which determinates the termination tolerance. Convergence threshold is set to 1E-05.

weighted.mean

Boolean flag, that indicates whether a weighted mean or a least square fit is used to summarize the loading matrix. The default value is set to FALSE.

robust

Boolean flag, that ensures non-constant results. Default value is TRUE.

minNoise

Value, minimal noise assumption. Default value is 0.0001.

correction

Value that indicates whether the covariance matrix should be corrected for negative eigenvalues which might emerge from the non-negative correlation constraints or not. Default = O (means that no correction is done), 1 (minimal noise (0.0001) is added to the diagonal elements of the covariance matrix to force positive definiteness), 2 (Maximum Likelihood solution to compute the nearest positive definite matrix under the given non-negative correlation constraints of the covariance matrix)

laplacian

Boolean flag, indicates whether a Laplacian prior for the factor is employed or not. Default value is FALSE.

centering

Indicates whether the data is "median" or "mean" centered. Default value is "median".

spuriousCorrelation

Numeric value in the range of [0,1] that quantifies the suppression of spurious correlation when using the Laplacian prior. Default value is 0 (no suppression). Note, that this parameter is only active when the laplacian parameter is set to 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

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