m2loglik.normexp {limma}R Documentation

Normal + Exponential Log-Likelihood

Description

Marginal log-likelihood of foreground values for normal + exponential model. This function is called by backgroundCorrect and is not normally called directly by the user.

Usage

m2loglik.normexp(theta,foreground,background=NULL,background.matrix=NULL)

Arguments

theta numeric vector of parameters
foreground numeric vector of foreground intensities
background optional vector of background intensity values
background.matrix option design matrix for regression on background values

Details

Computes the likelihood based on the $normal(μ,σ^2)+exponential(α)$ convolution model for the foreground intensities. The last two elements of theta are $log(σ)$ and $log(α)$. The other elements are the vector $β$.

The vector $β$ is related to $μ$ through $μ=Xβ$ if $X=$background.matrix is non-null. Otherwise $μ=β_1+β_2$background if background is non-null. If both background and background.matrix are null, then $μ=β_1$.

Value

Numeric scalar giving minus twice the log-likelihood

Author(s)

Gordon Smyth

See Also

fit.normexp, signal.normexp

An overview of normalization and background correction functions is given in 4.Normalization.


[Package limma version 1.8.6 Index]