Using R to evaluate DGE for differential expression

Moderated statistical tests for assessing differences in tag abundance. (2007). Robinson MD, Smyth GK. Bioinformatics. 23(21):2881-7. PMID: 17881408

The authors of this paper develop a statistical test using a negative binomial distribution to model noise in the data. They release R code (available at bioinf.wehi.edu.au/resources/) to support their treatment, but it is uncommented, and not functional as is.

Here I apply the code and examine the results in a sample data set.

At the website above you can find a tar archive called: msage_0.7.tar.gz. I can't get the package to install in R, so I simply unpack it and use the .R files directly. In addition, the code calls a function (decker.R) which is not included in the distribution. However, it is available here:

# set working directory and load library functions
setwd("E:/cry1/Solexa/Smyth")
source("fitNBP.R")
source("msage.R")

CategoryR