qBio I

Thursday, September 6th, 2018 – Thursday, December 13th, 2018
Tuesdays and Thursdays, 5:30 PM – 7:00 PM
Location: C-200 Weill Auditorium (or as indicated; n.b.: first day meets in A-950)
1300 York Avenue; 2nd Floor, Room C-200 (unless otherwise noted)
Midterm Exam: Thursday, November 1st (5:30 pm – 7:30 pm) in Room C-200
Course Directors:

Teaching Assistants (qbiotas2018@gmail.com):
Office hours and locations:

  • Shana Bergman
    Wednesdays, 12pm, E-511
  • Scott Kulm
    Fridays, 10am, Belfer 1422
  • Nakul Yadav
    Mondays, 7pm, CRC 1st floor

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

Class Sessions and Lecture Notes

  1. Quantifying a Sample Distribution part I (R code)
    Thursday, September 6th, 2018
    (note: class meets in A-950)

    summary statistics, quantiles, SD vs. SEM; introduction to swirl

  2. Quantifying a Sample Distribution part II (R code)
    Tuesday, September 11th, 2018

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

  3. Probability Density Functions and the Normal Distribution part I (R code)
    Thursday, September 13th, 2018

    binomial, Poisson, and normal distributions, testing for normality (part I): an introduction to formal statistical tests

  4. Probability Density Functions and the Normal Distribution part II (R code)
    Tuesday, September 18th, 2018

    testing for normality (part II): qqplots vs. formal tests

  5. Lab #1: Practical R (Rmd code)
    Thursday, September 20th, 2018

    Common data structures (vectors); Markdown; strategizing Jeop-R-dy

  6. Jeop-R-dy heats
    Monday-Friday, September 24-28, 2018
    (Note: times and locations TBA)

  7. Confidence Intervals and Contingency Tables (R code)
    Tuesday, October 2nd, 2018

    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

  8. Final Jeop-R-dy
    Thursday, October 4th, 2018

  9. p-Values and Formal Statistical Testing (R code)
    Tuesday, October 9th, 2018

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

  10. Lab #2: Practical R
    Thursday, October 11th, 2018

    common data structures continued (lists and dataframes); understanding Type I error rates

  11. Statistical Power and Experimental Design (R code)
    Tuesday, October 16th, 2018

    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

  12. Multiple Hypothesis Testing and Non-parametric Tests (R code)
    Thursday, October 18th, 2018

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

  13. Midterm Exam Review (led by TAs)
    Tuesday, October 23rd, 2018

  14. Bayesian Methods (R code)
    Thursday, October 25th, 2018

    how to incorporate prior knowledge into statistical models

  15. Midterm Exam
    Thursday, November 1st, 2018

  16. Lab #3: Practical R (R code)
    Tuesday, November 6th, 2018

    the role of simulation in statistics, non-parametric tests, exploring the optimal stopping problem

  17. Correlation vs. Linear Regression (R code)
    Thursday, November 8th, 2018

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

  18. Code quality
    Tuesday, November 13th, 2018

  19. Fitting Model Parameters to Data (R code)
    Thursday, November 15th, 2018

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

  20. Thanksgiving Break: No class
    Week of November 20th, 2018
    Tuesday, November 27th, 2018

  21. Quantitative Comparison of Models and ANOVA part I (R code)
    Thursday, November 29th, 2018

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

  22. Quantitative Comparison of Models and ANOVA part II (R code) | Problem Set 3
    Tuesday, December 4th, 2018

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

  23. Principal Component Analysis (R code)
    Thursday, December 6th, 2018

    data transformation and data reduction methods

  24. Introduction to ggplot2
    Tuesday, December 11th, 2018

    publication-quality graphics with ggplot