This package implements a method for normalization, testing, and false discovery rate estimation for RNAsequencing data. The description of the method is in Li J, Witten DM, Johnstone I, Tibshirani R (2012). Normalization, testing, and false discovery rate estimation for RNAsequencing data. Biostatistics 13(3): 52338. We estimate the sequencing depths of experiments using a new method based on Poisson goodnessoffit statistic, calculate a score statistic on the basis of a Poisson loglinear model, and then estimate the false discovery rate using a modified version of permutation plugin method. A more detailed instruction as well as sample data is available at http://www.stanford.edu/~junli07/research.html. In this version, we changed the way of calculating log foldchange for twoclass data. The FDR estimation part remains unchanged.
Package details 


Author  Jun Li 
Date of publication  20121010 15:36:34 
Maintainer  Jun Li <[email protected]> 
License  GPL (>= 2) 
Version  1.1.2 
Package repository  View on CRAN 
Installation 
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