Differential Expression Analysis Using a Bottom-Up Model
Differential expression analysis using a bottom-up model
Get posterior samples of a parameter
An S4 class to represent summarised counts and the output of Bayesian ...
Compute the test statistic
Generic for altering the initValues slot
Generic for the altering output slot.
Generic for the altering setReplicates slot.
Generic for altering the stepSizes slot.
Get values of the tuned step sizes.
Given count data from two conditions, it determines which transcripts are differentially expressed across the two conditions using Bayesian inference of the parameters of a bottom-up model for PCR amplification. This model is developed in Ndifon Wilfred, Hilah Gal, Eric Shifrut, Rina Aharoni, Nissan Yissachar, Nir Waysbort, Shlomit Reich Zeliger, Ruth Arnon, and Nir Friedman (2012), <http://www.pnas.org/content/109/39/15865.full>, and results in a distribution for the counts that is a superposition of the binomial and negative binomial distribution.