Schedule 2019
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:
- Jason Banfelder (jbanfelder@rockefeller.edu)
- Luce Skrabanek (las2017@med.cornell.edu)
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
-
Introduction to R part I | R code
Tuesday, September 3rd, 2019 -
Introduction to R part II | R code
Thursday, September 5th, 2019
(Note: class starts at 6pm) -
Introduction to R part III | R code
Tuesday, September 10th, 2019 -
Introduction to R part IV | R code
ablation.xlsx | ablation.csv
Thursday, September 12th, 2019 -
Quantifying a Sample Distribution | R code
Tuesday, September 17th, 2019
summary statistics, SD vs. SEM, measurement variation vs. biological variation -
R Markdown | Rmd file | HTML file
Thursday, September 19th, 2019 -
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 -
Group sessions
Thursday, September 26th, 2019 -
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 -
Code Quality | R Styles Evolution
Thursday, October 3rd, 2019 -
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 -
Problem Set #1: Understanding Type I error rates | Group sessions
Thursday, October 10th, 2019 -
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 -
Group sessions
Thursday, October 17th, 2019 -
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 -
Group sessions
Thursday, October 24th, 2019 -
Problem Set #2: the optimal stopping problem | R code
Tuesday, October 29th, 2019 -
Midterm Exam Review (led by TAs)
Wednesday, October 30th, 2019
(Note: held from 6-8pm, in B210-B212) -
Midterm Exam
Thursday, October 31st, 2019 -
Bayesian Methods | R code
Tuesday, November 5th, 2019
how to incorporate prior knowledge into statistical models -
Correlation vs. Linear Regression | R code
Tuesday, November 12th, 2019
introduction to modeling in R; why is not the whole story -
Fitting Model Parameters to Data | R code
Thursday, November 14th, 2019
non-linear regression, a statistical view of curve fitting, confidence intervals revisited -
No class
Tuesday, November 19th, 2019
Joshua Lederberg – John von Neumann Symposium: Towards Quantitative Biology -
Group sessions
Thursday, November 21st, 2019 -
Thanksgiving Break: No class
Week of November 25th, 2019 -
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 -
Midterm review
Thursday, December 5th, 2019 -
Principal Component Analysis | R code
Thursday, December 10th, 2019
data transformation and data reduction methods -
Graphics with ggplot2
Thursday, December 12th, 2019