Publicly available microarray data (August 18, 2005). Category: Data mining

A working paper in the Johns Hopkins Biostatistics department,

• Searching for Differentially Expressed Gene Combinations. Marcel Dettling, Edward Gabrielson, and Giovanni Parmigiani
  www.bepress.com/cgi/viewcontent.cgi?article=1077&context=jhubiostat

uses two microarray data sets to test their methodology. I could not access the first data set, but the second data set, a microarray experiment associated with a NEJM publication

• Gene Expression Profiles in Hereditary Breast Cancer. Ingrid Hedenfalk, David Duggan, Yidong Chen, Michael Radmacher, Michael Bittner, Richard Simon, Paul Meltzer, Barry Gusterson, Manel Esteller, Mark Raffeld, Zohar Yakhini, Amir Ben-Dor, Edward Dougherty, Juha Kononen, Lukas Bubendorf, Wilfrid Fehrle, Stefania Pittaluga, Sofia Gruvberger, Niklas Loman, Oskar Johannsson, Håkan Olsson, Benjamin Wilfond, Guido Sauter, Olli-P. Kallioniemi, Åke Borg and Jeffrey Trent

which has supplemental information on the web at

• research.nhgri.nih.gov/microarray/NEJM_Supplement/

The documentation for the data file is at

• Description of Gene Expression Ratio Data File for BRCA Experiments. Prepared by Yidong Chen, May 16, 2001.
  research.nhgri.nih.gov/microarray/NEJM_Supplement/read_me.pdf

and the data file itself is at

• research.nhgri.nih.gov/microarray/NEJM_Supplement/Images/nejm_brca_release.txt

When I get a chance, I will try to import this data into R and Bioconductor and see if I can get a few simple analyses out.

This webpage was written by Steve Simon and was last modified on 07/08/2008.