Semester Project

Statistical Analysis of Genetic Data

Math 155

Jo Hardin

Spring 2008

 

 

A major part of your grade will consist of carrying out a complete analysis of a set of microarray data.  The semester project will be broken up into parts due periodically throughout the semester.  At the end of the semester you will give a 15-20 minute presentation on the data.  Additionally, your final assignment will consist of a webpage which organizes the various parts of the analysis.

 

Some general thoughts on creating a website

 

Project

Comments

Due

Collect Data

(email me data)

Thurs 1/31/08

Write-up Data

(create website)

Thurs 2/7/08

Enter Data into R

 

Thurs 2/14/08

Normalize Data

Some helpful R commands

Fri 2/29/08 5pm

Experimental Design

 

Fri 3/7 5pm

Differential Expression

       Limma

       SAM & Multiple Comparisons

 

 

Loading & using siggenes

 

Mon 3/31 5pm

Fri 4/11 5pm

Clustering

       Hierarchical Clustering

       Partitioning Around Medoids (PAM)

 

 

Fri 4/18 5pm

Fri 4/25 5pm

Classification

       Prediction Analysis of Microarrays (PAM)

 

 

Wed 5/7 5pm

Presentation (15-20 minutes)

 

Thurs 5/1/08 & Tues 5/6/08

Final Project / Discussion / Website

 

Wed 5/7/08

 

 

 

 

 

Examples of projects from Spring 2008:

 

Austen Head (2008): Subramanian S, et al. (2008).  "MicroRNA expression signature of human sarcomas." Oncogene 27(14):2015-26

 

Alison Kosel (2009): Simmons CP, et al. (2007). “Patterns of Host Genome–Wide Gene Transcript Abundance in the Peripheral Blood of Patients with Acute Dengue Hemorrhagic Fever.” The Journal of Infectious Diseases 195(8):1097-1107.

 

Hilary Parker (2008): Subramanian S, et al. (2008).  "MicroRNA expression signature of human sarcomas." Oncogene 27(14):2015-26