m2loglik.normexp {limma} | R Documentation |
Marginal log-likelihood of foreground values for normal + exponential model and its derivatives.
This function is called by backgroundCorrect
and is not normally called directly by the user.
m2loglik.normexp(theta,foreground,background=NULL,background.matrix=NULL) sumloglik(theta,foreground,background) grsumloglik(theta,foreground,background)
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 |
Computes minus twice the log-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 $μ=β_1$.
m2loglik.normexp
is minus-twice the log-likelihood.
sumloglik
is minus the log-likelihood.
grsumloglik
is the gradient vector and grloglik
the gradient components for individual spots.
Numeric scalar giving minus twice the log-likelihood
There are undocumented arguments in the function grloglik
.
These will disappear soon.
Jeremy Silver and Gordon Smyth
An overview of normalization and background correction functions is given in 4.Normalization
.