Materials to reproduce test set bias analysis.
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README.txt
download_esets.R
testsetbias.Rmd

README.txt

Thanks for replicating the analysis from Patil, et. Al. (2014).

1. Please ensure that the necessary packages are installed on your
system.

	The following can be installed from CRAN:

	colorspace, ggplot2, plyr, knitr, tables

	The following can be installed from Bioconductor using the code
	source("http://bioconductor.org/biocLite.R")
	biocLite(PAKCAGE_NAME)

	genefu, affyPLM, pamr, survcomp

	The following can be installed from github using the devtools package:
	e.g. install_github("MetaGx", username="bhaibeka", ref="master")	

	MetaGx

	(See installation instructions at)
	https://github.com/jtleek/tspreg
	https://github.com/bhaibeka/MetaGx

2. Once all dependencies are installed, open R and make the test_set_analysis directory
your working directory. Then run the following commands

	library(knitr)
	knit2html("testsetbias.Rmd")

The whole processs should take about 35 minutes to run. The resulting file
"testsetbias.html" can be opened in a web browser to view the analysis
and figures from the paper.

Thank you!