Discussion Sessions with T.A. Bokan Bao (dates TBA) 
Week 2 
Friday October 12, 23:30 p.m. in AP&M 6402

Tutorial on Matlab and R. Worksheets:
Matlab, R

Week 5 or 6 
Location and date TBA

Week 7 or 8 
Location and date TBA

Week 10 or 11 
Location and date TBA

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

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. 3 

continued (slides 2745)

Expected values (1.4) and Variance (1.5)

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

Week 2 
Mon. Oct. 8 

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

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

Mendel's Laws, crossovers and recombination rates, Haldane's Mapping Function
(slides)

Poisson distribution and crossovers (Ewens & Grant 1.3.7, 4.14.2)
(slides 117)

Wed. Oct. 10 

Poisson distribution, continued (slides 1822)
For now, skip slides 2331 on the Exponential and Gamma Distributions; we will cover these topics later.
LanderWaterman shotgun sequencing statistics (5.1)
(slides)

Week 3 
Mon. Oct. 15 
Maximum Likelihood Estimates (8.18.3)
(slides)
Continuous distributions
(slides 114)

Continuous distributions (1.81.10, 4.3)

Uniform distribution

Cumulative distribution function

Wed. Oct. 17 

Exponential and gamma distributions (1.10, 4.3) (slides 14end)
Normal distribution and Central Limit Theorem (1.10, 2.10)
(slides 123)

Normal distribution

Approximating binomial distribution by normal distribution

Week 4 
Mon. Oct. 22 

continued (rest of slides)

Central Limit Theorem
Hypothesis testing, intro:
(slides)

Distribution of the maximum of n random variables (2.11)

Long repeats (5.4) and hypothesis tests (3.4)

Wed. Oct. 24 

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

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

Week 5 
Mon. Oct. 29 

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)

Probability generating functions intro (1.7, 1.11, 2.3)

Wilcoxon signed rank test (3.8.3)

MannWhitney test (3.8.2)

Wed. Oct. 31 
 Nonparametric hypothesis tests, continued (slides)

Week 6 
Mon. Nov. 5 
 Nonparametric hypothesis tests, continued (rest of slides)
Microarrays:
(slides)

Wed. Nov. 7 
Midterm

Week 7 
Mon. Nov. 12 
Microarrays, continued (rest of slides)
Chisquared hypothesis tests:
(slides)

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

Wed. Nov. 14 

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

Number of occurrences of a word (5.7) and a motif (5.9) allowing overlaps
(slides)

Week 8 
Mon. Nov. 19 

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

Wed. Nov. 21 

Week 9 
Mon. Nov. 26 

Markov chains, continued (rest of slides)

Wed. Nov. 28 
Principal Components Analysis
(slides)

Week 10 
Mon. Dec. 3 

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

Wed. Dec. 5 

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

Week 11 
Wed. Dec. 12 
Final exam, 36 p.m.
