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Date |
Book reading |
Topic |
Other reading |
Assignment |
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Tues 1/22 |
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Intro to class |
Syllabus / schedule / powerpoint history of microarrays |
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Thurs 1/24 |
Chapters 1, 2 (skip 2.2, 2.3,) |
Intro to Genetics |
Campbell & Heyer: pgs 107-114 Genomish McLachlan, Do, & Ambroise: pgs 18-23 http://www.bio.davidson.edu/courses/genomics/chip/chip.html if you want more info: animation: http://gcat.davidson.edu/Pirelli/index.htm fact sheet: http://www.ncbi.nlm.nih.gov/About/primer/microarrays.html |
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Tues 1/29 |
Chapter 3 (skip 3.2, 3.5) |
Image Processing |
Stekel: chapter 4 |
* 5 questions for Professor Hoopes (typed) * Install MAGIC Tool onto your computer (if you’d like to use your own computer): http://www.bio.davidson.edu/projects/magic/magic.html |
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Thurs 1/31 |
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DeRisi et al. (just the first few pages) |
* HW #1 |
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Tues 2/5 |
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Gridding |
Gridding continued… |
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Thurs 2/7 |
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R – put R on your own computer (if you want to use your own computer). We will be using R for the rest of the semester. |
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Tues 2/12 |
12 (skip 12.4 & 12.5) |
Normalization |
Stekel: chapters 5 |
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Thurs 2/14 |
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* HW #3 |
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Tues 2/19 |
10.1-10.5 |
Normalization |
Stekel: chapter 6 Yang et al. 2002 |
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Thurs 2/21 |
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Tues 2/26 |
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“Normality” |
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Thurs 2/28 |
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* HW #4 (due Friday 2/29 5pm) * Normalizing (due Friday 2/29 5pm) |
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Tues 3/4 |
8 |
Experimental Design |
Kerr & Churchill 2001 Simon et al. pgs 17-23 |
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Thurs 3/6 |
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In class activity / handout |
* HW #5 (due Friday 3/7 5pm) * Exp Design (due Friday 3/7 5pm) |
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Tues 3/11 |
7 |
Differential Expression |
You should already know the material in chapters 4, 5, 6 |
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Thurs 3/13 |
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* Summary Q (due Friday 3/14 5pm) |
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Tues 3/18 |
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Spring Break! |
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Thurs 3/20 |
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Tues 3/25 |
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SAM |
SAM article: |
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Thurs 3/27 |
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* HW #6 (due Monday 3/31 5pm) * Limma modeling (due Monday 3/31 5pm) |
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Tues 4/1 |
9, 13.1-13.5 |
Multiple Comparisons |
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Thus 4/3 |
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Tues 4/8 |
11 |
Distances / Intro to Clustering |
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Thurs 4/10 |
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R code for HW 7 Data for HW 7 Loading & using siggenes |
* HW #7 (due Friday 4/11 5pm) * SAM & Multiple Comparisons (due Friday 4/11 5pm) |
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Tues 4/15 |
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PAM (clustering) |
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Thurs 4/17 |
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* HW #8 (due Friday 4/18 5pm) * Hierarchical Clustering (due Friday 4/18 5pm) |
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Tues 4/22 |
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PAM (classification) |
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Thurs 4/24 |
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R code for PAM Clustering project |
* HW #9 (due Friday 4/25 5pm) * PAM Clustering (due Friday 4/18 5pm) |
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Tues 4/29 |
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ROC curves / Cross validation |
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Thurs 5/1 |
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Presentations! |
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Tues 5/6 |
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Presentations! |
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Wed 5/7 |
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Final Project is Due (webpage, which will include a 1-2 page summary that might be called a “discussion section” if you were writing up a paper for a journal article). |
* PAM Classification (due Wednesday 5/7 5pm) * Final Project (due Wednesday 5/7 5pm) |
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