This folder contains R programs and a data file for generating Figure 5 of "Error estimates for the analysis of differential expression from RNA-seq count data", namely a set of comparison plots of false discovery rates attained by several RNA-seq software packages.  As an added bonus it also generates a parallel set of plots of false positive rates (not shown in the paper).  

To run, use setwd() to set the working directory to the path of the folder containing these files.  Then execute

> source("FDR_and_FPR_Fig_5.R")

WARNING: because RNA-seq packages are slow, it takes about 1/2 an hour to run on a MacBook air, for instance.  