Skip to content

leekgroup/testsetbias

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

8 Commits
 
 
 
 
 
 

Repository files navigation

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!

About

Materials to reproduce test set bias analysis.

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages