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Here we describe the Broad GDAC standardized data runs, which aim to produce versioned packages representing a frozen snapshot of all TCGA analysis data at a given time:

  • Cast in a form amenable to immediate algorithmic analysis (no additional data preparation required)
  • Which provides a consistent point of reference for analysis and citation by marker papers and users of TCGA data
  • Towards a formal definition of what constitutes a given tumor dataset
  • While minimizing redundant effort across centers and groups to download & prepare data for further analysis
  • And enhancing provenance and reproducibility

The standardized data packages may be accessed as described here.  More background information on this effort is available in this presentation from the April 2011 TCGA meeting, which was refined in subsequent presentations on May 12th and May 19th, as well as the 2011 NCI TSM meeting and ongoing discussions with TCGA collaborators.  Please note that due to ongoing software development and manual data collection efforts, no RNA-Seq or MAF data was included in the Nov 15, 2011 stddata runs.  RNA-Seq data were bundled in the Nov 28 stddata run, and both RNA-Seq and MAF data will be bundled with the December 2011 runs.

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