This web page was produced as an assignment for a course on Statistical Analysis on Microarray Data at Pomona College (return to index)

Austen Head – Math 155 – website last modified May 7, 2008

I am currently enrolled in a class offered at Pomona College called Statistical Analysis of Genetic Data (Math 155). To pursue this field of study, each student was required to search the Stanford Microarray Database publications (SMD publications) publications and find an article that was of interest to the student. I chose an article called “MicroRNA Expression Signature of Human Sarcomas” (Oncogene abstract where you can purchase the article) (SMD listing with access to the original data). In this class we use the software R.

(Assignment # – due date – finished/incomplete)

(PROJECT ASSIGNMENT #1 – Jan 31 – Finished)

citation and abstract for MicroRNA Expression Signature of Human Sarcomas

information about the data

(PROJECT ASSIGNMENT #2 – Feb 7 – Finished)

get the article (copyrighted)

description of the experiment undertaken to collect data

(PROJECT ASSIGNMENT #3 – Feb 14 – Finished)

how did authors filter, normalize, segment the data

interesting things about the dataset

printout of first 5 rows of data from R

(PROJECT ASSIGNMENT #4 – Feb 29 – Finished)

my normalization & tests of normalization

(PROJECT ASSIGNMENT #5 – Mar 7 – Finished)

update and organize website

description of experimental design of study

(PROJECT ASSIGNMENT #6 – Mar 31 – Finished – MODIFIED APRIL 11)

Top ten significant genes

(PROJECT ASSIGNMENT #7 – Apr 11 – Finished)

SAM

(PROJECT ASSIGNMENT #8 – April 21 – Finished)

Dendrograms

(PROJECT ASSIGNMENT #9 – April 25 – Finished)

PAM Clustering

(PROJECT ASSIGNMENT #10 – May 7 – Finished)

PAMr Classification

(Et Cetera – May 7)

Discussion

Presentation PDF PowerPoint

(R-CODE – modified May 7)

R code that I have so far

This website was designed by Austen Head.

Email: austen [dot] head [at] pomona [dot] edu

Pomona Math Department