Fall 2015
Stat 565: Statistical Methods for Analyzing Genomic Data (3 credits)
Schedule:
Pre-requisites:
Instructor:
Office:
Phone:
e-mail:
Office Hours:
MWF 2:10-3:00 pm JKSN 53
Stat 412/ 423 or Permission by Instructor
Nairanjana (Jan) Dasgupta
Neill 403
335-3736
dasgupta@wsu.edu
M 3-4, W 1-2, Th 2-3
References (used but not required)
1. Statistical Analysis of Gene Expression Data, Ed. Speed, CRC Press, 2003
2. The Analysis of Gene Expression Data, Ed. Parmigiani, Garrett, Irizarry, Zeger, Springer 2003
3. Exploration and Analysis of DNA Microarray and Protein data, Amaratatunga, Cabrera, Wiley, 2004
4. Statistics for Microarrays, Wit and McClure, Wiley, 2004
5. R for SAS and SPSS users, Muenchen, Springer, 2009
6. Case Studies in BioConductor, Gentleman, Hahne, Springer 2008
Other texts and papers will be added over the semester
Topics by week:
Week 1: Overview for this class
a. Statistical topics
b. Data input and simple statistics in R
Week 2: What is the Biological Problem at hand?
a. A brief description of the Central Dogma of Molecular Biology
b. Some very basic biology related to data
Week 3: Data Types
a. Microarrays
b. Proteomic data
c. Rna-seq data
d. Metabolomic data
e. Genome Wide Association studies
Week 4: Image Analysis
a. Basic of how we get from image to data
b. Sources of variation for data (systematic and stochastic)
Week 5 &6: Normalizing Data
a. Why Normalization?
b. LOESS non-parametric regression methods
c. Stochastic error versus systematic errors
Week 7: Design Issues:
a. Replication: how many and why
b. Design Matrix
c. Optimality Criterion
d. Writing out design matrices
Week 8: Differential Expression (classical)
a. Hypothesis tests
b. Type I and II errors
c. Parametric and Non-parametric Test
d. t-tests and ANOVA Your Midterm will be around this time:
Week 9: Differential Expression (Bayes)
a. moderated t
b. moderated F
c. Empirical Bayes Method
Week 10: The question of multiplicity adjustment, FWE, PCE or FDR? Discuss:
a. Bonferroni corrections,
b. False Discovery Rates, FDR
c. Sequential Bonferroni, the Holm adjustment
d. Westfall and Young’s Mult-test adjustments
Week 11 and 12: Clustering, pros and cons, theoretical implications of:
a. Hierarchical versus Non-hierarchical clustering
b. K-means clustering, Self Organizing Maps
c. Hierarchical Clustering and Dendograms
d. Model Based Clustering
e. Principal Components
f. Multi-dimensional Scaling
Week 13: Discriminant Analysis
Week 14 and 15: GWAS and Wrap up
Labs: Over the semester we will have data analysis labs where you will bring your laptop to class and we will
run R to analyze data.
Description of Required Assignments and Grading policy:
MIDTERM EXAM (100 points)
FINAL EXAM (Comprehensive)
PROJECTS
HOMEWORK
30%.
30%.
20%.
20%.
A (93%-100%); A- (90%-93%); B+ (87%-90%); B (83%-87%) B- (80%-83%); C+ (77%-80%); C (73%-77%); C(70%-73%) D+ (66%-70%); D (60%-66%); F(0%-60%)
No late assignments will be accepted.
2
Student Learning Outcomes:
Student Learning Outcomes for this
course:
At the end of this course, students
should be able to:
Understand the structure of genomic
data and the distributional
assumptions
Understand specific nuances of this
type of data and why normalization
is required
Analyze this type of data
Be able to independently analyze
data and synthesize results
Course Topics/Dates
The following
topic(s)/dates(s) will
address this outcome:
This will be covered in
Week 3
Will be covered in Week 4
Will be covered from Week
7 onwards to the end of
class
From week 1 to week 14
this will be the underlying
deliverable of this class
Evaluation of Outcome:
This outcome will be evaluated
primarily by:
Homework assignments and
midterm exam and written
projects
Homework assignments and
midterm exam and written
projects
Homework assignments and
written projects as well as both
midterm and final exam
Independent project and final
exam.
Attendance Policy: I require attendance for my classes and if you have an excused reason why you
missed class you are responsible for making up the work.
3
WSU Reasonable Accommodation Statement
“Students with Disabilities: Reasonable accommodations are available for students with a
documented disability. If you have a disability and need accommodations to fully participate in this
class, please either visit or call the Access Center (Washington Building 217; 509-335-3417) to
schedule an appointment with an Access Advisor. All accommodations MUST be approved through
the Access Center. For more information contact a Disability Specialist on your home campus:
Pullman or WSU Online: 509-335-3417
http://accesscenter.wsu.edu, Access.Center@wsu.edu
http://gradschool.wsu.edu/FacultyStaff/Committee/
WSU Academic Integrity Statement:
Academic integrity is the cornerstone of the university. You assume full responsibility for the content
and integrity of the academic work you submit. You may collaborate with classmates on assignments,
with the instructor's permission. However the guiding principle of academic integrity shall be that
your submitted work, examinations, reports, and projects must be your own work. Any student who
violates the University's standard of conduct relating to academic integrity will be referred to the
Office of Student Conduct and may fail the assignment or the course. You can learn more about
Academic Integrity on your campus using the URL listed in the Academic Regulations section or to
http://conduct.wsu.edu/academic-integrity-policies-and-resources. Please use these resources to
ensure that you don’t inadvertently violate WSU's standard of conduct. Also please be familiar with
the GSC requirements for graduate students http://gradschool.wsu.edu/FacultyStaff/Committee/
Safety and Emergency Notification
Washington State University is committed to enhancing the safety of the students, faculty, staff, and
visitors. It is highly recommended that you review the Campus Safety Plan (http://safetyplan.wsu.edu/)
and visit the Office of Emergency Management web site (http://oem.wsu.edu/) for a comprehensive
listing of university policies, procedures, statistics, and information related to campus safety, emergency
management, and the health and welfare of the campus community. Be familiar with the Graduate
School statement at: http://gradschool.wsu.edu/FacultyStaff/Committee/
4