Discussion Sessions with T.A. George Armstrong (dates TBA) 
Week 2 
Wednesday October 9, 4:305:50 p.m. in AP&M B402

Tutorial on Matlab and R. Worksheets:
Matlab, R

Week 5 or 6 
Thursday, October 31, 3:003:50pm 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 6, 33:50 p.m. in AP&M 6402

Lectures: Week 1 
Mon. Sep. 30 
Website and syllabus
Review of discrete random variables:
(slides 127)
[revised 10/3]

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. 2 

continued (slides 28)

Expected values (1.4) and Variance (1.5)

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

Week 2 
Mon. Oct. 7 
Mendel's Laws and Gene mapping:

Note that there are two sets of slides to download 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)
[revised 10/13]

For now, skip slides 23end on the Exponential and Gamma Distributions; we will cover these topics later.

Wed. Oct. 9 
LanderWaterman shotgun sequencing statistics (5.1)
(slides)
[revised 10/13]
Conditional Probability and Bayes' Theorem
(slides 416)

Week 3 
Mon. Oct. 14 

Bayes' Theorem continued (review + slides 1724)
Continuous distributions:
(slides 126)
[revised again 10/14]

Continuous distributions (1.81.10, 4.3)

Uniform distribution

Cumulative distribution function

Exponential and gamma distributions (1.10, 4.3)

Wed. Oct. 16 

continued (rest of slides)
Maximum Likelihood Estimates (8.18.3)
(slides)
Normal distribution and Central Limit Theorem (1.10, 2.10):
(slides 110)
[revised 10/13]

Normal distribution

Approximating binomial distribution by normal distribution

Week 4 
Mon. Oct. 21 

continued (rest of slides)

Central Limit Theorem
Hypothesis testing, intro:
(slides 112)

Distribution of the maximum of n random variables (2.11)

Long repeats (5.4) and hypothesis tests (3.4)

Wed. Oct. 23 

continued (review + slides 1320; delaying slides 2324)
Hypothesis tests for the normal distribution:
(slides 119)

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

Confidence intervals (3.3.2)

Week 5 
Mon. Oct. 28 

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 14)

Probability generating functions intro (1.7, 1.11, 2.3)

Wilcoxon signed rank test (3.8.3)

MannWhitney test (3.8.2)

Wed. Oct. 30 
 Nonparametric hypothesis tests, continued (rest of slides)

Week 6 
Mon. Nov. 4 
Microarrays
(slides 136)
[revised 11/4]

Wed. Nov. 6 
Midterm

Week 7 
Mon. Nov. 11 
Veterans Day

Wed. Nov. 13 
Microarrays, continued (rest of slides)
Chisquared hypothesis tests:
(slides 117)

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

Week 8 
Mon. Nov. 18 

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)

Wed. Nov. 20 
Linear Algebra Review:
Markov chains (4.54.9, 11.{1,2,4,6}):

Week 9 
Mon. Nov. 25 

Markov chains, continued (832)

Wed. Nov. 27 

Markov chains, continued (rest of slides)
Principal Components Analysis:
(slides 120)

Week 10 
Mon. Dec. 2 

PCA, continued (rest of slides)
Linear Regression (8.4.3):
(slides 15)

Wed. Dec. 4 
 Linear regression, continued (rest of slides)
Analysis of Variance (9.59.7, 13.3.7):
(slides)

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

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