Department of Bioinformatics and Computational Biology

Education:MicroarrayCourse

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Analysis of Microarray Data

GS01 0163, Fall 2010

Schedule: Tuesday and Thursday, 3:00 - 4:30, GSBS Library (BSRB S3.8351). We will meet in the GSBS Conference Room (BSRB S3.8355) on Tuesday, October 7 and Thursday, December 2.

Contents


Lecture Notes

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    

Homework Assignments

Due Tuesday, 28 September
Assignment 1
Due Tuesday, 12 October
Assignment 2
Due Tuesday, 26 October
Assignment 3
Supplements required for Assignment 3 include:

Useful Links

Previous Incarnation: GS01 0163, Fall 2009

Lecture Notes

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  
Analysis.pdf Lecture 20 , 5 November 2009 Pathway Analysis (Romesh Stanislaus) Analysis.pdf 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  

Homework Assignments

Due Tuesday, 15 September
Assignment 1
Due Thursday, 22 September
Assignment 2
Due Thursday, 15 October
Assignment 3
Supplements required for Assignment 3 include:

Previous Incarnation: GS01 0163, Fall 2007

Lecture Notes

Lecture Title Printable (B/W) Auxiliary FIles
Lecture 0 , 28 August 2007 Administration, Syllabus, etc. PDF file  
Lecture 1 , 28 August 2007 The Structure of Affymetrix Data PDF file  
Lecture 2 , 30 August 2007 The Basics of dChip PDF file  
Lecture 3 , 4 September 2007 Gene Annotations: Linking Numbers to Biology PDF file  
6 September 2007 Live dChip Demo NA  
Lecture 4 , 11 September 2007 Cell Lines, Microarrays, Drugs and Documentation PDF file  
Lecture 5 , 13 September 2007 An Introduction to R PDF file  
Lecture 6 , 18 September 2007 More on R and Affymetrix Arrays PDF file sample.Rnw , sample.pdf , affyExample.pdf
Lecture 7 , 20 September 2007 Affymetrix, R, and BioConductor PDF file ma07.Rnw (source file)
Lecture 8 , 25 September 2007 Normalization and Affymetrix PDF file  
Lecture 9 , 27 September 2007 Normalization, Affy, and R PDF file  
Lecture 10 , 2 October 2007 Exploring Bioconductor PDF file ma10.Rnw (source file)
Lecture 11 , 4 October 2007 Differential Expression PDF file  
Lecture 12 , 9 October 2007 Rank-based tests of differential expression PDF file ma12.Rnw (source file)
Lecture 13 , 11 October 2007 Differential Expression, Borrowing, and Modelling PDF file  
Lecture 14 , 16 October 2007 Reporting Differential Expression PDF file  
18 October 2007 Ovarian Cancer Improv NA  
Lecture 16 , 23 October 2007 Clustering Microarray Data PDF file  
Lecture 17 , 25 October 2007 Applied Clustering PDF file  
Lecture 18 , 30 October 2007 Classification with Microarrays I PDF file  
Lecture 19 , 1 November 2007 Classification with Microarrays II PDF file  
Lecture 20 , 6 November 2007 Genome Browsing PDF file ma20.Rnw (source file) Agilent44K_1.0.zip (annotation package)
Lecture 21 , 8 November 2007 Comparing Microarray Analysis Methods PDF file  
Lecture 22 , 13 November 2007 Quantifying Glass Microarrays PDF file  
Lecture 23 , 15 November 2007 R and Glass Microarrays PDF file  
Lecture 24 , 20 November 2007 Design, Microarrays, and Proteomics PDF file  
Lecture 25 , 27 November 2007 Linear Models for Two-color Microarrays PDF file  
Lecture 26 , 29 November 2007 Time Series PDF file  
Lecture 27 , 4 December 2007 Meta-analysis of CLL PDF file  
Class 102705 b.ppt Lecture 28 , 6

December 2007

Pooling data across microarray experiments    

Homework Assignments

Due Tuesday, 11 September
Assignment 1
Due Thursday, 20 September
Assignment 2
Due Thursday, 4 October
Assignment 3
Supplements required for Assignment 3 include:
Due Tuesday, 23 October
Assignment 4
Due Thursday, 16 November
Assignment 5
Supplements required for Assignment 5 include:

Previous Incarnation: GS01 0163, Fall 2006

Lecture Notes

Lecture Title Printable (B/W)
Lecture 0 , 29 August 2006 Administration, Syllabus, etc. PDF file
Lecture 1 , 29 August 2006 The Structure of Affymetrix Data PDF file
Lecture 2 , 31 August 2006 The Basics of dChip PDF file
Lecture 3 , 5 September 2006 Gene Annotations: Linking Numbers to Biology PDF file
7 September 2006 Live dChip Demo NA
Lecture 4 , 12 September 2006 Introduction to R PDF file
Lecture 5 , 14 September 2006 R, Objects, and Affymetrix Arrays PDF file
Lecture 6 , 19 September 2006 Affymetrix, R, and BioConductor PDF file
Lecture 7 , 21 September 2006 Normalization and Affymetrix PDF file
Lecture 8 , 26 September 2006 Normalization, Affy, and R PDF file
Lecture 9 , 28 September 2006 Exploring Bioconductor PDF file
Lecture 10 , 3 October 2006 Differential Expression PDF file
Lecture 11 , 5 October 2006 Rank-based tests of differential expression PDF file
Lecture 12 , 10 October 2006 Differential Expression, Borrowing, and Modeling PDF file
Lecture 13 , 12 October 2006 Reporting Differential Expression PDF file
Lecture 14 , 17 October 2005 Genome Browsing PDF file
Lecture 15 , 19 October 2006 Comparing Microarray Analysis Methods PDF file
Lecture 16 , 24 October 2006 Quantifying Glass Microarrays PDF file
Lecture 17 , 26 October 2006 R and Glass Microarrays PDF file
Lecture 18 , 31 October 2005 A Two-color Case Study PDF file
Lecture 19 Extra , 2 November 2006 Notes on Homework 4 PDF file
Lecture 19 , 2 November 2006 Linear Models for Two-color Microarrays PDF file
Lecture 20 , 7 November 2006 Clustering Microarray Data PDF file
Lecture 21 , 9 November 2006 Applied Clustering PDF file
Lecture 22 , 14 November 2006 Classification with Microarrays I PDF file
Lecture 23 , 16 November 2006 Classification with Microarrays II PDF file
Lecture 24 , 21 November 2005 Design, Microarrays, and Proteomics PDF file
Lecture 25 , 28 November 2006 Meta-analysis of CLL PDF file
Lecture 26 , 30 November 2006 Time Series PDF file
Class 102705 b.ppt Lecture 27 , 5

December 2006

Pooling data across microarray experiments  

Homework Assignments

Due Tuesday, 12 September
Assignment 1
Due Tuesday, 19 September
Assignment 2
Due Date Thursday, 4 October
Assignment 3
Supplements required for Assignment 3 include:
Due Thursday, 26 October
Assignment 4
Due Thursday, 16 November
Assignment 5
Supplements required for Assignment 5 include:
Due Thursday, 7 December
Assignment 6
Supplements required for Assignment 6 include:

Previous Incarnation: GS01 0163, Fall 2005

Lecture Notes

Lecture Title Printable (B/W)
Lecture 0, 30 August 2005 Administration, Syllabus, etc. PDF file
Lecture 1, 30 August 2005 The Structure of Affymetrix Data PDF file
Lecture 2, 1/6 September 2005 The Basics of dChip PDF file
Lecture 3, 8 September 2005 Gene Annotations: Linking Numbers to Biology PDF file
Lecture 4, 13 September 2005 Introduction to R PDF file
Lecture 5, 15 September 2005 BioConductor and Affymetrix Arrays PDF file
Lecture 6, 20 September 2005 Affymetrix, R, and BioConductor PDF file
Lecture 7, 27 September 2005 Normalization and Affymetrix PDF file
Lecture 8, 29 September 2005 Normalization, Affy, R, and Glass PDF file
Lecture 9, 4 October 2005 Differential Expression PDF file
Lecture 10, 6 October 2005 Rank-based tests of differential expression PDF file
Lecture 11, 11 October 2005 Differential expression and modelling PDF file
Lecture 12, 13 October 2005 Differential expression and borrowing PDF file
Lecture 13, 18 October 2005 Microarray in R, Start to Finish PDF file
Lecture 14, 20 October 2005 Comparing Analysis Methods PDF file
[http://bioinformatics.mdanderson.org/MicroarrayCourse/Lectures05/Li Zhang talk microarray class2005.ppt Lecture

15], 25 October 2005

Guest Lecturer: Li Zhang

Modeling sequence dependence of microarray probe signals

 
Class 102705 b.ppt Lecture 16,

27 October 2005

Guest Lecturer: Jeff Morris

Pooling data across microarray experiments

 
Lecture 17, 1 November 2005 Quantifying Glass Microarrays PDF file
Lecture 18, 3 November 2005 R and Glass Microarrays PDF file
Lecture 19, 8 November 2005 A Two-color Case Study PDF file
Lecture 20, 10 November 2005 A Two-color Case Study (continued) PDF file
Lecture 21, 15 November 2005 Clustering Microarray Data PDF file
Lecture 22, 17 November 2005 Applied Clustering PDF file
Lecture 23, 22 November 2005 Design, Microarrays, and Proteomics PDF file
Lecture 24, 29 November 2005 Classification with Microarrays I PDF file
Lecture 25, 1 December 2005 Classification with Microarrays II PDF file
Lecture 26, 6 December 2005 Meta-analysis of CLL PDF file
Lecture 27, 8 December 2005 Time Series and Open Questions PDF file

Homework Assignments

Due Tuesday, 13 September
Assignment 1
Revised Due Date - Thursday, 29 September
Assignment 2
Due Thursday, 6 October
Assignment 3
Supplements required for Assignments 3 and 4 include:
Due Thursday, 13 October
Assignment 4
Due Thursday, 1 December
Assignment 5
Supplements required for Assignment 5 include:

Previous Incarnation: GS01 0163, Fall 2004

Lecture Notes

Lecture 1, 31 August 2004.
Introduction to Microarrays.
Lecture 2, 2 September 2004.
The Structure of Microarrays.
Lecture 3, 7 September 2004.
Quantifying cDNA Microarrays.
Lecture 4, 9 September 2004.
Quantifying Affymetrix Microarrays.
Lecture 5, 14 September 2004.
BioConductor and Affymetrix Arrays.
Lecture 6, 16 September 2004.
R and Glass Microarrays.
Lecture 7, 21 September 2004.
Normalization and Affymetrix.
Lecture 8, 23 September 2004.
Normalization, Affy, R, and Glass.
Lecture 9, 28 September 2004.
Differential Expression.
Lecture 10, 30 September 2004.
Rank-based tests of differential expression.
Lecture 11, 5 October 2004.
Differential expression and modelling.
Lecture 12, 7 October 2004.
Differential expression and borrowing.
Lecture 13, 12 October 2004.
Biological interpretation.
14 October 2004
Class cancelled.
Lecture 14, 19 October 2004.
Biology: Functions and Networks.
Lecture 15, 21 October 2004.
Regulatory Networks.
Lecture 16, 26 October 2004.
Designing Microarray Experiments.
Lecture 17, 28 October 2004.
Clustering Microarray Data I.
Lecture 18, 2 November 2004.
Clusters, Partitions, and Silhouettes.
Lecture 19, 4 November 2004.
Applied Clustering.
Lecture 20, 9 November 2004.
Classification I.
Lecture 21, 11 November 2004.
Classification II.
Lecture 22, 16 November 2004.
Predicting clinical outcome.
Lecture 23, 23 November 2004.
Meta-analysis.
Lecture 24, 30 November 2004.
Meta-analysis of CLL Studies.
Lecture 25, 7 December 2004.
Time Course Studies
Lecture 26, 9 December 2004.
Open Questions
Lecture 26 Bonus, 9 December 2004.
Analysis of Proteomic Spectra

Homework Assignments

Due Tuesday, 7 September
Assignment 1
Due Tuesday, 21 September
Assignment 2. To complete this, you must also download the data set for assignment 2.
Due Thursday, 7 October
Assignment 3. To complete this, you must also download the data set for assignment 3.