RosR ChIP-chip processing

ChIP-chip processing pipeline for Tonner et al. "A regulatory hierarchy controls the dynamic transcriptional response to extreme oxidative stress in archaea."

• This repository contains the code necessary to recereate table S2 from the manuscript
• Raw data file can be downloaded from GEO: GSE58696

Dependencies

• R (version 2.5 recommended) - knitr, MeDiChI (available here: http://cran.r-project.org/src/contrib/Archive/MeDiChI/)

Steps to recreate table:

• download raw data from GEO, and unpack the data to data/chip
• run the command 'R CMD Sweave preprocessing_0258_all_none_densityLoess_max100.Rnw'
• Download table S5 from Sharma et al. BMC Genomics 2012, and save 'all_data_H2O2' as data/rosr_h2o2_exp.csv
• from R, run 'knit2html(rosr-timcourse-analysis.Rmd)' with the knitr package