We used TCGA GBM data from the following archives: 

expression Agilent: 
/unc.edu_GBM.AgilentG4502A_07_1.1.3.0/
/unc.edu_GBM.AgilentG4502A_07_1.2.2.0/
/unc.edu_GBM.AgilentG4502A_07_1.3.2.0/
/unc.edu_GBM.AgilentG4502A_07_1.4.2.0/
/unc.edu_GBM.AgilentG4502A_07_2.10.0.0/
/unc.edu_GBM.AgilentG4502A_07_2.5.3.0/
/unc.edu_GBM.AgilentG4502A_07_2.6.2.0/
/unc.edu_GBM.AgilentG4502A_07_2.7.2.0/
/unc.edu_GBM.AgilentG4502A_07_2.8.1.0/

expression affy:
/broad.mit.edu_GBM.HT_HG-U133A.1.3.0/
/broad.mit.edu_GBM.HT_HG-U133A.2.3.0/
/broad.mit.edu_GBM.HT_HG-U133A.3.3.0/
/broad.mit.edu_GBM.HT_HG-U133A.4.3.0/
/broad.mit.edu_GBM.HT_HG-U133A.5.3.0/
/broad.mit.edu_GBM.HT_HG-U133A.6.3.0/
/broad.mit.edu_GBM.HT_HG-U133A.7.3.0/

Copy number harvard:
/hms.harvard.edu_GBM.HG-CGH-244A.1.5.0/
/hms.harvard.edu_GBM.HG-CGH-244A.2.4.0/
/hms.harvard.edu_GBM.HG-CGH-244A.3.5.0/
/hms.harvard.edu_GBM.HG-CGH-244A.4.5.0/
/hms.harvard.edu_GBM.HG-CGH-244A.6.3.0/
/hms.harvard.edu_GBM.HG-CGH-244A.8.3.0/
/hms.harvard.edu_GBM.HG-CGH-244A.9.3.0/

Copy number MSKCC:
/mskcc.org_GBM.HG-CGH-244A.1.4.0/
/mskcc.org_GBM.HG-CGH-244A.2.3.0/
/mskcc.org_GBM.HG-CGH-244A.3.2.0/
/mskcc.org_GBM.HG-CGH-244A.4.1.0/
/mskcc.org_GBM.HG-CGH-244A.5.2.0/
/mskcc.org_GBM.HG-CGH-244A.6.1.0/
/mskcc.org_GBM.HG-CGH-244A.7.1.0/
