R: EBSeq: RNA-Seq Differential Expression Analysis on both gene...

EBSeq_NingLeng-package {EBSeq}

R Documentation

EBSeq: RNA-Seq Differential Expression Analysis on both gene and isoform level

Description

In 'EBSeq_NingLeng-package,' a Negative Binomial-beta model was built to analyze the RNASeq data. We used the empirical bayes method and EM algrithom.

Details

Package:	EBSeq_NingLeng
Type:	Package
Version:	1.0
Date:	2011-06-13
License:	What license is it under?
LazyLoad:	yes

Author(s)

Ning Leng, Christina Kendziorski

Maintainer: Ning Leng <nleng@wisc.edu>

References

Ning Leng, John A. Dawson, James A. Thomson, Victor Ruotti, Anna I. Rissman, Bart M.G. Smits, Jill D. Haag, Michael N. Gould, Ron M. Stewart, and Christina Kendziorski. EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics (2013)

Examples

data(GeneMat)
GeneMat.small = GeneMat[c(1:10,511:550),]
Sizes = MedianNorm(GeneMat.small)
EBOut = EBTest(Data=GeneMat.small, 
	Conditions=as.factor(rep(c("C1","C2"), each=5)), 
	sizeFactors=Sizes, maxround=5)