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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

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'

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