BIOS 567:
Statistical Methods for Microarray Data
Monday, April 27, 2009 Assignment
- Read pp. 217-231 in Sorin Draghici's Data Analysis for DNA Microarrays.
- Homework 5 is due Wednesday, April 29.
Wednesday, April 22, 2009 Assignment
- Read Darlene R. Goldstein, Debashis Ghosh, Erin M. Conlon. (2002) Statistical issues in the clustering of gene expression data. Statistica Sinica, 12:219-240.
- Homework 5 is due Wednesday, April 29.
- Final exam is Monday, May 4 - Carter Conference room is reserved from 8AM-11AM..
Monday, April 20, 2009 Assignment
- Read Eisen MB, Spellman, Brown PO, Botstein D. (1998) Cluster analysis and display of genome-wide expression patterns. PNAS, 95:14863-14868.
Wednesday, April 15, 2009 Assignment
- Read pp. 278-309 in Sorin Draghici's Data Analysis for DNA Microarrays.
Monday, April 13, 2009 Assignment
- Read pp. 265-278 in Sorin Draghici's Data Analysis for DNA Microarrays.
- Homework 4 is due Wednesday, April 15.
Wednesday, April 8, 2009 Assignment
- Homework 4 is due Wednesday, April 15.
Monday, April 6, 2009 Assignment
- Read pp.331-342 in Sorin Draghici (2003) Data Analysis Tools for DNA Microarrays.
- Read Rafael A. Irizarry, Bridget Hobbs, Francois Collin, Yasmin D. Beazer-Barclay, Kristen J. Antonellis, Uwe Scherf, and Terence P. Speed. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 2003 4: 249-264.
Wednesday, April 1, 2009 Assignment
- Read Cheng Li and Wing Hung Wong. Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proceedings of the National Academy of Sciences, 98(1):31-36.
Monday, March 30, 2009 Assignment
- Read
W.-m Liu, R. Mei, X. Di, T. B. Ryder, E. Hubbell, S. Dee, T. A. Webster, C. A. Harrington, M.-h. Ho, J. Baid, and S. P. Smeekens. Analysis of high density expression microarrays with signed-rank call algorithms. Bioinformatics 2002 18: 1593-1599.
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Wednesday, March 25, 2009 Assignment
- Read Earl Hubbell, Wei-Min Liu, and Rui Mei. Robust estimators for expression analysis. Bioinformatics 2002 18: 1585-1592.
Monday, March 23, 2009 Assignment
- Read B.M. Bolstad, R.A Irizarry, M. Åstrand, and T.P. Speed (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
Wednesday, March 4, 2009 Assignment
- Read the following Bioconductor vignettes by Yee Hwa Yang and Sandrine Dudoit:
Introduction to the Bioconductor marray package: Input component;
Introduction to the Bioconductor marray package : Classes structure component;
Normalization: Bioconductor's marray package
Monday, March 2, 2009 Announcement
- The university is closed due to inclement weather. Class will not be held today. Today's office hour will be held tomorrow from 1-2PM.
Wednesday, February 25, 2009 Assignment
- Read pp.311-331 in Sorin Draghici (2003) Data Analysis Tools for DNA Microarrays.
- Homework 3 is due Wednesday, March 4.
Monday, February 23, 2009 Assignment
- Read Yee Hwa Yang, Sandrine Dudoit, Percy Luu, David M. Lin, Vivian Peng, John Ngai, and Terence P. Speed (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research, Feb 15;30(4):e15.
Monday, February 16, 2009 Assignment
- Homework 2 is due Monday, February 23.
Wednesday, February 11, 2009 Assignment
- Read section 12.3.1 (pp. 320-322) of Sorin Draghici (2003) Data Analysis Tools for DNA Microarrays.
- Homework 2 is tentatively due Wednesday, February 18.
Monday, February 9, 2009 Assignment
- Read Chapter 3 of Sorin Draghici (2003) Data Analysis Tools for DNA Microarrays.
Wednesday, February 4, 2009 Assignment
- Read Danh V. Nguyen, A. Bulak Arpat, Naisyin Wang, Raymond J. Carroll (2002) DNA Microarray Experiments: Biological and Technological Aspects. Biometrics, 8:701-717.
Monday, February 2, 2009 Assignment
- Read Chapter 2 of Sorin Draghici (2003) Data Analysis Tools for DNA Microarrays.
Wednesday, January 28, 2009 Assignment
- Read the Preface and Chapter 1 of Sorin Draghici (2003) Data Analysis Tools for DNA Microarrays.
- Reminder: Homework 1 is due Monday, February 2.
Monday, January 26, 2009 Assignment
- Read chapter 12 of An Introduction to R by W.N. Venables, D.M. Smith, and the R Development Core Team.
- Homework 1 will be due Monday, February 2.
Wednesday, January 21, 2009 Assignment
- Read chapters 8-11 of An Introduction to R by W.N. Venables, D.M. Smith, and the R Development Core Team.
- Homework 1 will be due Monday, February 2.
Wednesday, January 14, 2009 Reading Assignment
- Read chapters 4, 5, 6, and 7 of An Introduction to R by W.N. Venables, D.M. Smith, and the R Development Core Team.
Monday, January 12, 2009 Reading Assignment
- Read chapters 1, 2, and 3 of An Introduction to R by W.N. Venables, D.M. Smith, and the R Development Core Team.
