Meeting Summary for 11/6/08

We went over PCA and its applications to microarray data (http://sysbio.soe.ucsc.edu/Pubs/psb00.pdf).

For next week we decided to look SVD with each of us looking at specific aspects

Jang : ICA and NCA

Mike : Excerpts of Strang's lecture;
Application :
Alter O, Brown PO, Botstein D. (2000) Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci U S A, 97, 10101-6.

Ina : Matlab Commands for SVD

Archana : Types of Matrices (Definite, Positive Definite etc)

Meeting Summary for 9/8/08

Today we talked about data pre-processing for microarrays. We reviewed chapter 12 in Sorin Draghici's "Data Analysis Tools for DNA Microarrays". We also looked at some slides from Dr. Kim's class on the topic. (Archana can you post these as a comment?)

For next time we're going to each look up some review papers on normalization techniques, and hopefully study the pros and cons of each. Archana will look for some information pertaining to chip-chip data. I'm going to review my notes from Stafford's class on M-A plots. Jang is going to summarize the distribution plot he sent in the email last week.

We'll also begin our discussion of hypothesis testing.

Meeting Agenda for 9/8/08

Please add comments to this post to modify the agenda.

1. (Main topic) Discuss data pre-processing for DNA microarray data. Sources include but are not limited to the Knudsen, Draghici and Speed books on my desk.
2. (Archana) Discuss binomial distribution for GO term enrichment.
3. (All) Discuss where the Gamma distribution is used in biology.