Gene expression preprocessing
Gene expression processing pipeline used in: Sharma et al., 2012, BMC Genomics 13:351; Tonner et al., 2015, PLOS Genetics, 11(1):e1004912.
- This repository contains the code necessary to normalize 2-color Agilent gene expression microarray data.
- Example data files from Sharma et al., 2012, are included for demonstration purposes.
Dependencies
- R (version 2.15.2):
- limma - http://www.bioconductor.org/packages/release/bioc/html/limma.html
- maDB - http://www.bioconductor.org/packages//2.7/bioc/html/maDB.html
- RColorBrewer
- yaml
- LaTex
- Sweave
Steps to run pipeline:
- To run the demo, use raw Aglient feature extraction files in the repository folder, 'raw/'
- To run on your own data, download raw data from GEO, create a folder called 'raw/' and unpack into that directory
- To run the demo, use metadata file 'metadata.txt'. To run on your own data, generate a metadata file modeled on the repository metadata example file.
- Run the command 'R CMD Sweave preprocessing.Rnw'