3. Image from Gene-Chips (Micorrrays)

5. Statistics for microarray analysis (SMA)
Method: Lowess
Goal: adjust systematic bias
Assumption: changes roughly symmetric at all intensities within the region considered

8. Hierarchical clustering
Technically, Eisen uses average-link agglomerative hierarchical clustering.
Similarity between genes is measured using a Pearson correlation coefficient.
Where to download the software:

9. Why cluster?
Place genes with similar expression profiles into clusters.
What is the gene’s function?
Place experiments / samples with similar expression profiles into clusters.
What is the expression profile of a particular disease or phenotype?