| Lecture | Title | Printable (B/W) | Auxiliary Files |
|---|---|---|---|
| Lecture 0, 1 September 2009 | Administration, Syllabus, etc. | PDF file | Programming Survey (pdf) |
| Lecture 1, 1 September 2009 | The Structure of Affymetrix Data | PDF file | |
| Lecture 2, 3 September 2009 | The Basics of dChip | PDF file | |
| Lecture 3, 8 September 2009 | Gene Annotations: Linking Numbers to Biology | PDF file | |
| Lecture 4, 10 September 2009 | Cell Lines, Microarrays, Drugs and Documentation | PDF file | |
| Lecture 5, 15 September 2009 | An Introduction to R | PDF file | |
| Lecture 6, 17 September 2009 | Sweave, More on R, and Affy. Arrays | PDF file | sample.Rnw, sample.pdf, |
| Lecture 7, 22 September 2009 | Affymetrix, R, and BioConductor | PDF file | |
| Lecture 8, 24 September 2009 | Normalization and Affymetrix | PDF file | |
| Lecture 9, 29 September 2009 | Normalization, Affy, and R | PDF file | |
| Lecture 10, 1 October 2009 | Differential Expression | PDF file | |
| Lecture 11, 6 October 2009 | Differential Expression, Borrowing, and Modelling | PDF file | |
| Lecture 12, 8 October 2009 | Reporting and Comparing Differential Expression | PDF file | |
| Lecture 13, 13 October 2009 | Design, Microarrays, and Proteomics | PDF file | |
| Lecture 14, 15 October 2009 | Linear Models, Design Matrices, and TCGA | PDF file | |
| Lecture 15, 20 October 2009 | Hierarchical Clustering | PDF file | |
| Lecture 16, 22 October 2009 | Applied Clustering | PDF file | |
| Lecture 17, 27 October 2009 | Classification with Microarrays I | PDF file | |
| Lecture 18, 29 October 2009 | Classification with Microarrays II | PDF file | |
| Lecture 19, 3 November 2009 | Genome Browsing | PDF file | |
| Lecture 20, 5 November 2009 | Pathway Analysis (Romesh Stanislaus) | PDF file | |
| Lecture 21, 10 November 2009 | Gene Set Enrichment Analysis | PDF file | |
| Lecture 22, 12 November 2009 | Batch Effects | PDF file | |
| Lecture 23, 17 November 2009 | Frozen Barcodes | PDF file | |
| Lecture 24, 19 November 2009 | Combining Data Across Affy Platforms | PPT file | |
| Lecture 25, 24 November 2009 | SNP Arrays | PDF file | |
| Lecture 26, 1 December 2009 | Next Generation Sequencing | PDF file | |
| Lecture 27, 3 December 2009 | Literature Discussion | PDF file |