Instructors - Jennifer Weller and Jeff Solka
Meeting Place - Discovery Hall 185

Meeting Time - 4:30 pm - 7:10 pm Wednesdays

Important Dates
First day of classes January 24
Last day to drop with no tuition penalty February 8
Last day to add classes February 8
Last day to drop February 25
Spring Break March 13 - March 20
Last day of classes May 7
Reading Days (Monday all day, Tuesday until 4:30 p.m.) May 9 - 10
Exam period (beginning 4:30 p.m. on Tues., May 10) May 10 - 18
Grades available via Patriot Web May 10
Degree conferral date May 21, 2005

Course Structure - Students will be introduced to both concepts and practical examples for handling and analyzing the data sets arising from large-scale microarray experiments. General analysis tools will include R, and the Bioconductor packages in its library, and Matlab, as well as software packages developed for handling specific analysis problems. Each instructor will lecture for one hour of each class meeting, and there will be a 30-minute practical demonstration of some of the tools discussed at the end of each class session. Homework problems will be assigned to reinforce concepts and develop skills needed for analyzing relevant data sets. Many of the problems will come from the Amaratunga and Cabrera end of chapter problems. Students will give one presentation that comprises a critical discussion of a relevant journal article (the instructors will provide a list of articles from which students may select or a student may independently find an article, subject to the instructors' approval) and a second presentation that presents an original project, for which a report must be written and submitted following an approved format.

Course Description - The student will learn concepts underlying manufacture and experimental design for micro-array studies and numerous micro-array data analysis techniques including data normalization, visualization, discriminant analysis, dimensionality reduction, and clustering.
Course grades: There will be six homework assignments (50%), an in-class presentation of an article from the literature (20%), and an in-class presentation of a project (20%) with an accompanying written report (10%). All homework must be turned in as hard copy at the time it is due; no late assignments will be accepted (however the lowest grade of the six may be dropped). There are no 'extra credit' assignments.

Course Textbooks -
"Exploration and Analysis of DNA micorarray and protein array data" by Amaratunga, D., and Cabrera, J. from Wiley Series in Probability and Statistics, 2004. [abbreviated AC for chapter assignments]

"Analyzing Microarray Gene Expression Data: by McLachlan, GJ, Do, K-A, and Ambroise, C from Wiley series in Probability and Statistics, 2004. [abbreviated MDA for chapter assignments]

"Microarray Bioinformatics" by Stekel, D. from Cambridge University Press, 2003. [abbreviated Stek for chapter assignments]

Tentative Course Schedule -