qBio I

Tuesday, September 3rd, 2019 – Thursday, December 12th, 2019
Tuesdays and Thursdays, 5:30 PM – 7:00 PM
Location: C-200 Weill Auditorium
1300 York Avenue; 2nd Floor, Room C-200 (unless otherwise noted)
Midterm Exam: Thursday, October 31st, 2019 (5:30 pm – 7:30 pm) in Room C-200
Course Directors:

Teaching Assistants (qbio2019@zoho.com):

  • Scott Kulm
  • Sofia Avritzer
  • Josue Barnes
  • Cerise Tang

Office hours (11am-12pm):

  • Nov 1 - BB 216
  • Nov 8 - BB 216
  • Nov 15 - BB 216
  • Nov 22 - BB 216
  • Dec 6 - BB 216
  • Dec 13 - E-511

This course will be fully graded: (Honors, High Pass, Low Pass, Fail)

Class Sessions and Lecture Notes

  1. Introduction to R part I | R code
    Tuesday, September 3rd, 2019

  2. Introduction to R part II | R code
    Thursday, September 5th, 2019
    (Note: class starts at 6pm)

  3. Introduction to R part III | R code
    Tuesday, September 10th, 2019

  4. Introduction to R part IV | R code
    ablation.xlsx | ablation.csv
    Thursday, September 12th, 2019

  5. Quantifying a Sample Distribution | R code
    Tuesday, September 17th, 2019

    summary statistics, SD vs. SEM, measurement variation vs. biological variation

  6. R Markdown | Rmd file | HTML file
    Thursday, September 19th, 2019

  7. Probability Density Functions and the Normal Distribution | R code
    Tuesday, September 24th, 2019

    binomial, Poisson, and normal distributions, testing for normality: an introduction to formal statistical tests, qqplots vs. formal tests

  8. Group sessions
    Thursday, September 26th, 2019

  9. Confidence Intervals and Contingency Tables | R code
    Tuesday, October 1st, 2019

    t-tests, working with proportional data, why CIs are more informative than p-values, study types (retrospective, prospective, and cross sectional), working with rare events

  10. Code Quality | R Styles Evolution
    Thursday, October 3rd, 2019

  11. p-Values and Formal Statistical Testing | R code
    Tuesday, October 8th, 2019
    (Note: class starts at 6pm)

    duality between p-values and CIs, statistical vs. biological significance, choosing an appropriate α, type I and type II errors

  12. Problem Set #1: Understanding Type I error rates | Group sessions
    Thursday, October 10th, 2019

  13. Statistical Power and Experimental Design | R code
    Tuesday, October 15th, 2019

    why you cannot just add a few N to your dataset when p > 0.05, appreciating the economics (in time and money) of experimental design, statistical vs. biological significance revisited, designing experiments around hard-to-obtain samples

  14. Group sessions
    Thursday, October 17th, 2019

  15. Multiple Hypothesis Testing and Non-parametric Tests | R code
    Tuesday, October 22nd, 2019

    from Bonferroni to False Discovery Rate, dealing with non-normal data, t-tests re-visited

  16. Group sessions
    Thursday, October 24th, 2019

  17. Problem Set #2: the optimal stopping problem | R code
    Tuesday, October 29th, 2019

  18. Midterm Exam Review (led by TAs)
    Wednesday, October 30th, 2019
    (Note: held from 6-8pm, in B210-B212)

  19. Midterm Exam
    Thursday, October 31st, 2019

  20. Bayesian Methods | R code
    Tuesday, November 5th, 2019

    how to incorporate prior knowledge into statistical models

  21. Correlation vs. Linear Regression | R code
    Tuesday, November 12th, 2019

    introduction to modeling in R; why is not the whole story

  22. Fitting Model Parameters to Data | R code
    Thursday, November 14th, 2019

    non-linear regression, a statistical view of curve fitting, confidence intervals revisited

  23. No class
    Tuesday, November 19th, 2019
    Joshua Lederberg – John von Neumann Symposium: Towards Quantitative Biology

  24. Group sessions
    Thursday, November 21st, 2019

  25. Thanksgiving Break: No class
    Week of November 25th, 2019

  26. Quantitative Comparison of Models and ANOVA | R code | Problem Set #3
    Tuesday, December 3rd, 2019

    how to avoid over-fitting, F-test and AICs, F-tests as a means of parameter estimation

  27. Midterm review
    Thursday, December 5th, 2019

  28. Principal Component Analysis | R code
    Thursday, December 10th, 2019

    data transformation and data reduction methods

  29. Graphics with ggplot2
    Thursday, December 12th, 2019