fit.em: Probability of expresison from mixture distribution for a...

In metaArray: Integration of Microarray Data for Meta-analysis

Description

This core function fits two-component normal-uniform mixture distribution, and extracts probability of over/under expression for all samples in all genes.

Usage

  fit.em(x, cl, threshold=1e-06)

Arguments

x	A numeric vector, especially expression values for a particular gene.
cl	A vector of 0s and 1s. Use 1 for normal phenotype and 0 for non-normal phenotype. Note that this is the opposite of POE MCMC. If all samples are of unknown phenotype or of the same one, give vector of zeros. When class information is provided, conditional estimation of the mixture is applied.
threshold	Criterion for convergence in likelihood

Value

expr	Estimated POE
a	Minimum (adjusted) of Raw Expression
b	Maximum (adjusted) of Raw Expression
sigmasq	Estimated variance of normal component
mu	Estimated mean of normal component
Pi	Probability that the gene is over/under expressed on average across the samples
lik.rec	Trajectory of likelihood during EM

Author(s)

Debashis Ghosh <[e-mail]>, Hyungwon Choi <[e-mail]>

metaArray documentation built on April 29, 2020, 2:12 a.m.