Statistical Methods for Mapping Quantitative Trait Loci
Zhao-Bang Zeng and Brian S. Yandell

• Book Outline
  • Current Book Outline (ZBZ, 21 aug 2000)
  • Proposed Book Outline (ZBZ & BSY, 17 nov 2000)

• Chapter Handouts (mostly local access)
  • QTL Analysis
  • Microarray Data Analysis
• Return to Statistical Genomics References

QTL Analysis Handouts (local access only)

• Quantitative Trait Loci References

1. Introduction
2. QTL Mapping Data
3. Linkage Map Analysis
4. Quantitative Genetic Models [87k]
   • Modeling Epistasis [117k]
5. Single Marker Analysis [78k]
6. Interval Mapping (IM) [128k]
7. Composite Interval Mapping (CIM) [113k]
8. Multiple Interval Mapping (MIM) [122k]
9. A General View and Directions for Extension
   • Resampling with QTL [21k]
   • Bayesian Interval Mapping (BIM) [1.2M]
10. Dominant and Missing Marker Analysis
11. Multiple Trait Analysis [121k]

Microarray Data Analysis Handouts (local access only)

• Microarray Expression Data Analysis References
• Terry Speed Group Microarray Talks & Posters
  • includes image analysis, clustering & classification

1. Overview [19k]
   • Introduction to statistical genomics issues with microarray data (Newton Yandell et al 2001)
2. Biology Implications of Gene Expression Arrays
3. Microarray Image Analysis (Yang Speed; Wong)
   • extracting information from microarray images (Yang 2000)
   • normalization for cDNA microarray data (Yang et al. 2001)
4. Comparing Two Conditions (Chen et al; Dudoit et al.; Newton et al)
   • Mining for low-abundance transcripts in microarray data (Yandell et al. 2000) [2.2M]
5. Experimental Design for Microarrays (Kerr Churchill)
6. Principle Components and Microarray Experiments (Alter et al.; West et al.)
   • Discussion of singular value decomposition (Bates Goldstein 2000)
7. Clustering & Classification for Microarrays (Eisen et al; Dudoit et al; Tamayo et al.; Golub et al.)
   • Comparison of discrimination methods for the classification of tumors using gene expression data (Dudoit, Fridlyand, Speed 2000)
8. Microarrays in F2 and BC Experiments
   • QTL studies with microarrays (Lan ... Yandell 2000) [1.4M]
9. Microarrays and Congenic Lines