Image from Gene-Chips (Micorrrays) Statistics for microarray analysis (SMA)

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Presentation transcript:

Image from Gene-Chips (Micorrrays)

Statistics for microarray analysis (SMA) http://www.stat.berkeley.edu/users/terry/zarray/Software/smacode.html Method: Lowess Goal: adjust systematic bias Assumption: changes roughly symmetric at all intensities within the region considered

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: http://rana.lbl.gov/EisenSoftware.htm

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?