1. Analysis of Multiple Experiments TIGR Multiple Experiment Viewer (MeV) Joseph White DFCI January 24,2008

4. The Expression Matrix is a representation of data from multiple microarray experiments. Each element is a log ratio (usually log 2 (Cy5 / Cy3) ) Red indicates a positive log ratio, i.e, Cy5 > Cy3 Green indicates a negative log ratio , i.e., Cy5 < Cy3 Black indicates a log ratio of zero, i. e., Cy5 and Cy3 are very close in value Gray indicates missing data Exp 1 Exp 2 Exp 3 Exp 4 Exp 5 Exp 6 Gene 1 Gene 2 Gene 3 Gene 4 Gene 5 Gene 6

6. Expression Vectors As Points in ‘Expression Space’ Experiment 1 Experiment 2 Experiment 3 Similar Expression -0.8 -0.6 0.9 1.2 -0.3 1.3 -0.7 Exp 1 Exp 2 Exp 3 G1 G2 G3 G4 G5 -0.4 -0.4 -0.8 -0.8 -0.7 1.3 0.9 -0.6

7. Distance and Similarity -the ability to calculate a distance (or similarity, it’s inverse) between two expression vectors is fundamental to clustering algorithms -distance between vectors is the basis upon which decisions are made when grouping similar patterns of expression -selection of a distance metric defines the concept of distance

9. Distance is Defined by a Metric 4.2 1.4 -1.00 -0.90 Euclidean Pearson(r*-1) Distance Metric : D D

10. Normal distribution X = μ (mean of the distribution) σ = std. deviation of the distribution

13. GeneChip Oncology Database

14. GeneChip Oncology Database