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

2. Today’s lab Complete tutorial
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

11. GEO Datasets

13. GEO Datasets (old interface)

14. GEO Datasets (new interface)

15. Check distribution (normalization) and experimental design

16. Clustering (Algorithms and Parameters)

17. GEO Datasets: Analysis

18. GEO Profiles

19. GEO Profiles

20. GEO Profiles

21. GEO Profiles

22. GEO Profiles

23. BRB Array Tools