normalMM {CEDA}

Performing empirical Bayes modeling on limma results

Description

This function perform an empirical Bayes modeling on log fold ratios and return the posterior log fold ratios.

Usage

normalMM(data, theta0, n.b = 5, d = 10)

Arguments

data

A numeric matrix containing limma results and log2 gene expression levels that has a column nameed 'lfc' and a column named 'exp.level.log2'

theta0

Standard deviation of log2 fold changes under permutations

n.b

Number of bins, default is 5 bins

d

Number of times for fitting mixture model using different starting values, default is 10

Value

A numeric matrix containing limma results, RNA expression levels, posterior log2 fold ratio, log p-values, and estimates of mixture model