gseconvert

The purpose of this utility is to take raw, heterogenous gene expression data (GSE files) from GEO and output a normalized matrix, with genes as columns and experiments as rows, for conducting gene expression meta-analyses such as described in some of our papers:

• GAMMA: Global Microarray Meta-analysis

Requirements

• R language (tested on 2.13.0), including RScript, on your PATH
• Python 2.x, also on PATH
• GNU Make and GNU grep (needs to support -P option)
• ~150 GB free disk space

Usage

First, download GSEs from NCBI's FTP servers, GEO and Entrez Gene metadata, and R package dependencies by running:

make download

Alternatively if you've already downloaded the GSEs, you can symlink data/GSE to a flat directory containing the GSEs and download the other dependencies individually (see the Makefile).

Now make the matrix for the species of your choice by running, e.g.:

make species-matrix SPECIES="Caenorhabditis elegans"

or for the platform of your choice:

make platform-matrix PLATFORM="GPL200"

being sure to surround the species/platform of interest by quotes. The resulting matrices (raw and quantile normalized) will be output into the data/ directory.

License

Copyright (C) 2011 Oklahoma Medical Research Foundation

Distributed under the Eclipse Public License.