Discussion Sessions with T.A. Bokan Bao (dates TBA) 
Week 2 
Friday October 13, 23:30 p.m. in AP&M 6402

Tutorial on Matlab and R. Worksheets:
Matlab, R

Week 5 or 6 
Monday November 6, 3:304:20 p.m. in AP&M 6402

Week 7 or 8 
TA review cancelled, added more linear algebra review to lecture instead

Week 10 or 11 
Friday December 8, 22:50 p.m. in AP&M 6402

Lectures: Week 1 
Mon. Oct. 2 
Website, syllabus, and background survey
Review of discrete random variables
(slides 125):

Probability density functions (Sec. 1.2)

Joint pdf (2.1, 2.2, 2.5)

Conditional pdf (2.6)

Combinations and permutations

Mass spec

Binomial (1.3.2) and multinomial (2.4.2) distributions

Wed. Oct. 4 
Review of discrete random variables, continued: (slides 2646)

Expected values (1.4) and Variance (1.5)

Geometric distribution (1.3.5) and Negative Binomial Distribution (1.3.6)

Week 2 
Mon. Oct. 9 

continued (rest of slides)
Mendel's Laws and Gene mapping:

Crossovers and Recombination rates
(slides)

Poisson distribution and crossovers (Ewens & Grant 1.3.7, 4.14.2)
(slides 116)
For now, skip slides 2331 on the Exponential and Gamma Distributions; we will cover these topics later.

Note that we are finishing last week's slides, and then two additional sets of slides are posted for today's lecture.

Wed. Oct. 11 

Poisson distribution, continued (slides 1722; skip slides 2331, we will do those topics later)
LanderWaterman shotgun sequencing statistics (5.1)
(slides 128)

Week 3 
Mon. Oct. 16 

continued (rest of slides)
Continuous distributions
(slides 119)

Continuous distributions (1.81.10, 4.3)

Uniform distribution

Cumulative distribution function

Exponential and gamma distributions (1.10, 4.3)

Wed. Oct. 18 

continued (rest of slides)
Maximum Likelihood Estimates (8.18.3)
(slides)
Normal distribution and Central Limit Theorem (1.10, 2.10)
(slides 110)

Week 4 
Mon. Oct. 23 

continued (rest of slides)

Approximating binomial distribution by normal distribution

Central Limit Theorem
Hypothesis testing, intro:
(slides 17)

Distribution of the maximum of n random variables (2.11)

Long repeats (5.4) and hypothesis tests (3.4)

Wed. Oct. 25 

continued (rest of slides)
Hypothesis tests for the normal distribution:
(slides 115)

z and ttests for the mean of a normal distribution (3.5.13.5.2)

Week 5 
Mon. Oct. 30 

continued (rest of slides)

Confidence intervals (3.3.2)

Binomial tests for p

Choosing n to control Type I and Type II errors
Nonparametric hypothesis tests:
(slides 14)

Probability generating functions intro (1.7, 1.11, 2.3)

Wilcoxon signed rank test (3.8.3)

MannWhitney test (3.8.2)

Wed. Nov. 1 
 Nonparametric hypothesis tests, continued (slides 528)

Week 6 
Mon. Nov. 6 
 Nonparametric hypothesis tests, continued (rest of slides)
Microarrays:
(slides 122)

Wed. Nov. 8 
Midterm

Week 7 
Mon. Nov. 13 
Microarrays, continued (rest of slides)
Chisquared hypothesis tests:
(slides 16)

Chisquared (1.10.5) and Ftests (9.5.2) for variance.

Wed. Nov. 15 

Chisquared tests for goodnessoffit (3.5.4) and association (3.5.5) (rest of slides)
Frequencies of words:

Week 8 
Mon. Nov. 20 

continued (rest of slides)
Markov chains (4.54.9, 11.{1,2,4,6}):

Wed. Nov. 22 

Week 9 
Mon. Nov. 27 

Markov chains, continued (rest of slides)

Wed. Nov. 29 
Principal Components Analysis
(slides 123)

Week 10 
Mon. Dec. 4 

PCA, continued (rest of slides)
Linear Regression (8.4.3)
(slides 17)

Wed. Dec. 6 

Demo 1 and rest of slides
Analysis of Variance (9.59.7, 13.3.7)
(slides)

This is included most years, but we did not have time for it.

Week 11 
Wed. Dec. 13 
Final exam, 36 p.m.
