EPIC450k_repro

Reproducible analysis of the manuscript Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array

---

Authors: Jean-Philippe Fortin, Tim Triche and Kasper Daniel Hansen

• Step 1: download raw data using the script scripts/download.sh. The raw IDAT files will be saved into the data_raw folder.
• Step 2: process the data using the script processing/preprocess.R. The processed data will be saved into the data_processed folder.
• Step 3: normalize the data with the 3 normalization scripts contained in the processing folder.
• Step 4: perform the analyses using the scripts contained in the analysis folder. The figures will be saved in the folder figures.