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 
Friday November 2, 23:20 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 7, 23:20 p.m. in AP&M 6402

Lectures: Week 1 
Mon. Oct. 1 
Website, syllabus, and background survey
Review of discrete random variables
(slides 125):
[slides revised again 11/23]

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 116)
[revised]

Distribution of the maximum of n random variables (2.11)

Long repeats (5.4) and hypothesis tests (3.4)

Wed. Oct. 24 

continued (slides 1720); delaying slides 2324
Hypothesis tests for the normal distribution:
(slides 122)
[revised]

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

Confidence intervals (3.3.2)

Week 5 
Mon. Oct. 29 

continued (rest of slides)

Binomial tests for p

Choosing n to control Type I and Type II errors.
Also the delayed slides 2324 from the previous set of slides.
Nonparametric hypothesis tests:
(slides 112)

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 13end)

Week 6 
Mon. Nov. 5 
Microarrays:
(slides 133)
[revised]

Wed. Nov. 7 
Midterm

Week 7 
Mon. Nov. 12 
Veterans Day

Wed. Nov. 14 
Microarrays, continued (rest of slides)
Chisquared hypothesis tests:
(slides 112)

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

Week 8 
Mon. Nov. 19 

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 116)

Wed. Nov. 21 

continued (slide 24; skipping motifs)
Linear Algebra Review:
Markov chains (4.54.9, 11.{1,2,4,6}):

Week 9 
Mon. Nov. 26 

Markov chains, continued (up to slide 35)

Wed. Nov. 28 

Markov chains, continued (rest of slides)
Principal Components Analysis
(slides 126)
[revised again 12/3]

Week 10 
Mon. Dec. 3 

PCA, continued (rest of slides)
Linear Regression (8.4.3)
(slides 111)

Wed. Dec. 5 
 Linear regression, continued (rest of slides)
Analysis of Variance (9.59.7, 13.3.7)
(slides)

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

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