| Discussion Sessions with T.A. George Armstrong (dates TBA) |
| Week 2 |
Wednesday October 9, 4:30-5:50 p.m. in AP&M B402
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Tutorial on Matlab and R. Worksheets:
Matlab, R
|
| Week 5 or 6 |
Thursday, October 31, 3:00-3:50pm 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, 3-3:50 p.m. in AP&M 6402
|
| Lectures: Week 1 |
| Mon. Sep. 30 |
Website and syllabus
Review of discrete random variables:
(slides 1-27)
[revised 10/3]
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Probability density functions (Sec. 1.2)
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Joint pdf (2.1, 2.2, 2.5)
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Conditional pdf (2.6)
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Combinations and permutations
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Mass spec
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Binomial (1.3.2) and multinomial (2.4.2) distributions
|
| Wed. Oct. 2 |
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continued (slides 28-)
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Expected values (1.4) and Variance (1.5)
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Geometric distribution (1.3.5) and Negative Binomial Distribution (1.3.6)
|
| Week 2 |
| Mon. Oct. 7 |
Mendel's Laws and Gene mapping:
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Note that there are two sets of slides to download for today's lecture.
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Mendel's Laws, crossovers and recombination rates, Haldane's Mapping Function
(slides)
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Poisson distribution and crossovers (Ewens & Grant 1.3.7, 4.1-4.2)
(slides)
[revised 10/13]
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For now, skip slides 23-end on the Exponential and Gamma Distributions; we will cover these topics later.
|
| Wed. Oct. 9 |
Lander-Waterman shotgun sequencing statistics (5.1)
(slides)
[revised 10/13]
Conditional Probability and Bayes' Theorem
(slides 4-16)
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| Week 3 |
| Mon. Oct. 14 |
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Bayes' Theorem continued (review + slides 17-24)
Continuous distributions:
(slides 1-26)
[revised again 10/14]
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Continuous distributions (1.8-1.10, 4.3)
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Uniform distribution
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Cumulative distribution function
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Exponential and gamma distributions (1.10, 4.3)
|
| Wed. Oct. 16 |
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continued (rest of slides)
Maximum Likelihood Estimates (8.1-8.3)
(slides)
Normal distribution and Central Limit Theorem (1.10, 2.10):
(slides 1-10)
[revised 10/13]
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Normal distribution
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Approximating binomial distribution by normal distribution
|
| Week 4 |
| Mon. Oct. 21 |
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continued (rest of slides)
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Central Limit Theorem
Hypothesis testing, intro:
(slides 1-12)
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Distribution of the maximum of n random variables (2.11)
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Long repeats (5.4) and hypothesis tests (3.4)
|
| Wed. Oct. 23 |
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continued (review + slides 13-20; delaying slides 23-24)
Hypothesis tests for the normal distribution:
(slides 1-19)
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z and t-tests for the mean of a normal distribution (3.5.1-3.5.2)
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Confidence intervals (3.3.2)
|
| Week 5 |
| Mon. Oct. 28 |
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continued (rest of slides)
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Binomial tests for p
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Choosing n to control Type I and Type II errors.
Also the delayed slides 23-24 from the previous set of slides.
Non-parametric hypothesis tests:
(slides 1-4)
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Probability generating functions intro (1.7, 1.11, 2.3)
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Wilcoxon signed rank test (3.8.3)
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Mann-Whitney test (3.8.2)
|
| Wed. Oct. 30 |
- Non-parametric hypothesis tests, continued (rest of slides)
|
| Week 6 |
| Mon. Nov. 4 |
Microarrays
(slides 1-36)
[revised 11/4]
|
| Wed. Nov. 6 |
Midterm
|
| Week 7 |
| Mon. Nov. 11 |
Veterans Day
|
| Wed. Nov. 13 |
Microarrays, continued (rest of slides)
Chi-squared hypothesis tests:
(slides 1-17)
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Chi-squared (1.10.5) and F-tests (9.5.2) for variance.
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| Week 8 |
| Mon. Nov. 18 |
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Chi-squared tests for goodness-of-fit (3.5.4) and association (3.5.5) (rest of slides)
Frequencies of words:
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Number of occurrences of a word (5.7) and a motif (5.9) allowing overlaps
(slides)
|
| Wed. Nov. 20 |
Linear Algebra Review:
Markov chains (4.5-4.9, 11.{1,2,4,6}):
|
| Week 9 |
| Mon. Nov. 25 |
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Markov chains, continued (8-32)
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| Wed. Nov. 27 |
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Markov chains, continued (rest of slides)
Principal Components Analysis:
(slides 1-20)
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| Week 10 |
| Mon. Dec. 2 |
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PCA, continued (rest of slides)
Linear Regression (8.4.3):
(slides 1-5)
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| Wed. Dec. 4 |
- Linear regression, continued (rest of slides)
Analysis of Variance (9.5-9.7, 13.3.7):
(slides)
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This is included some years, but we probably will not have time for it.
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| Week 11 |
| Fri. Dec. 13 |
Final exam, 3-6 p.m.
|