| Lecture | Title | Printable (B/W) | Auxiliary Files |
|---|---|---|---|
| Lecture 0, 31 August 2010 | Administration, Syllabus, etc. | PDF file | Programming Survey (pdf) |
| Lecture 1, 31 August 2010 | The Structure of Affymetrix Data | PDF file | |
| Lecture 2, 2 September 2010 | The Basics of dChip | PDF file | HG_U95A.CDF, HG_U95Av2.CDF |
| Lecture 3, 7 September 2010 | Gene Annotations: Linking Numbers to Biology | PDF file | |
| 9 September 2010 | Class Cancelled | ||
| Lecture 4, 14 September 2010 | Cell Lines, Microarrays, Drugs and Documentation | PDF file | |
| Lecture 5, 16 September 2010 | An Introduction to R | PDF file | |
| Lecture 6, 21 September 2010 | Sweave, More on R, and Affy. Arrays | PDF file | sample.Rnw, sample.pdf, |
| Lecture 7, 23 September 2010 | Affymetrix, R, and BioConductor | PDF file | |
| Lecture 8, 28 September 2010 | Normalization and Affymetrix | PDF file | |
| Lecture 9, 30 September 2010 | Differential Expression | PDF file | |
| Lecture 10, 5 October 2010 | Differential Expression, Borrowing, and Modelling | PDF file | |
| Lecture 11, 7 October 2010 | Reporting and Comparing Differential Expression | PDF file | |
| Lecture 12, 12 October 2010 | Design, Microarrays, and Proteomics | PDF file | |
| Lecture 13, 14 October 2010 | Linear Models, Design Matrices, and TCGA | PDF file | |
| Lecture 14, 19 October 2010 | Hierarchical Clustering | PDF file | |
| Lecture 15, 21 October 2010 | Applied Clustering | PDF file | |
| Lecture 16, 26 October 2010 | Classification with Microarrays I | PDF file | |
| Lecture 17, 28 October 2010 | Classification with Microarrays II | PDF file | |
| Lecture 18, 2 November 2010 | Genome Browsing | PDF file | Agilent44K_1.0.zip |
| Lecture 19, 4 November 2010 | Gene Set Enrichment Analysis | PDF file | |
| Lecture 20, 9 November 2010 | SNP Arrays | PDF file | |
| Lecture 21, 11 November 2010 | Batch Effects | PDF file | |
| Lecture 22, 16 November 2010 | Frozen Barcodes | PDF file | combinedSampleInfo.Rda |
| Lecture 23, 18 November 2010 | Combining Data Across Affy Platforms | PPT file | |
| Lecture 24, 23 November 2010 | Next Generation Sequencing 1 | ||
| Lecture 25, 30 November 2010 | Next Generation Sequencing 2 | ||
| Lecture 26, 2 December 2010 | Student Presentations 1: Data Preparation | ||
| Lecture 27, 7 December 2010 | Literature Discussion | PDF file | |
| Lecture 28, 9 December 2010 | Student Presentations 2: Gene Analysis Results |