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GEO—Gene Expression Omnibus

GEO—Gene Expression Omnibus. IBGP705 TA: Lee Cooper February 18, 2009. Today’s lab. Complete tutorial Email answers to questions to TA by 6pm today. Today’s lab. Accessing GEO GEO Datasets GEO Profiles The “Help” Section BRB Array Tools.

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GEO—Gene Expression Omnibus

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  1. GEO—Gene Expression Omnibus IBGP705 TA: Lee Cooper February 18, 2009

  2. Today’s lab • Complete tutorial • Email answers to questions to TA by 6pm today

  3. Today’s lab • Accessing GEO • GEO Datasets • GEO Profiles • The “Help” Section • BRB Array Tools

  4. Preparing and carrying out a microarray experiment

  5. Analysis of microarray data: clustering

  6. Potential problems with microarray

  7. Dealing with microarray problems • Best answer = normalization • Selection of normalization method/s • Software • Core lab

  8. Today’s lab: GEO • Various ways to visually examine microarray data to determine special need for normalization/ initial quality of data • Accessing GEO • GEO Datasets • GEO Profiles • The “Help” Section • BRB Array Tools

  9. Accessing GEO

  10. GEO Datasets

  11. GEO Datasets (old interface)

  12. GEO Datasets (new interface)

  13. Check distribution (normalization) and experimental design

  14. Clustering (Algorithms and Parameters)

  15. GEO Datasets: Analysis

  16. GEO Profiles

  17. GEO Profiles

  18. GEO Profiles

  19. GEO Profiles

  20. GEO Profiles

  21. BRB Array Tools

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