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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!