Analysis of Microarray Data: Lecture Notes

GS01 0163, Fall 2010

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