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Image from Gene-Chips (Micorrrays)

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.

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Image from Gene-Chips (Micorrrays)

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  1. Image from Gene-Chips (Micorrrays)

  2. 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

  3. 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

  4. 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?

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