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Biostatistics Grand Rounds March 13, 2001

Biostatistics Grand Rounds March 13, 2001. Discussion of Richard Simon’s talk: Using DNA Microarrays to Improve Cancer Diagnostic Classification. Outline. How is classification different? Is classification and/or clustering always appropriate? What’s the contribution of Statistics?

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Biostatistics Grand Rounds March 13, 2001

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  1. Biostatistics Grand RoundsMarch 13, 2001 Discussion of Richard Simon’s talk: Using DNA Microarrays to Improve Cancer Diagnostic Classification

  2. Outline • How is classification different? • Is classification and/or clustering always appropriate? • What’s the contribution of Statistics? • Are current analyses tools always appropriate?

  3. Classification • http://linus.nci.nih.gov/~brb/TechReport.htm “NN classifiers and DLDA had the lowest error rates, whereas FLDA had the highest” Dudoit, Fridlyand, and Speed (2001) JASA 97 77-87

  4. Clustering/Classification always appropriate? • Common problem: Find differentially expressed genes in two populations • A good design is important.

  5. Dye effect?

  6. Contribution of Statistics • “Not as simple as looking for red and green spots” • How big is big? • Critical exploration of Data • Garbage in, garbage out

  7. Saturation problem Probes reaching maximum in experiment 1 Scanner Chip PM MM Value 2 NV21a 354 25 46140 2 NV21b 564 57 46144 2 V21a 1004 83 46141 2 V21b 665 51 46139 1 NV100a 1917 328 46154 1 NV100b 1265 168 46160 1 V100a 3399 1085 46155 1 V100b 2267 446 46149

  8. Scanner Effect

  9. Remove Scanner Effect

  10. The red-green ratios can be spatially biased Top 2.5%of ratios red, bottom 2.5% of ratios green

  11. Anotherexample

  12. Looking for large FC

  13. Looking for large FC

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