smcclatchy
commented
6 years ago Initial sequence of topics selected from the outline are:
Day 1 Morning Introduction & welcome
Why we need better design. Resource saving. Suggested exercise: Think-pair-share. How can good experimental design help you to save money and time? How can it help your experiment to be reproducible? What are some ethical considerations of good experimental design?
Controlled experiments. Objectives, experimental units, treatment groups, independent replication, randomization, blinding. Suggested exercise: Review the Chick et al paper and data, and explore objectives, exp units, etc in both the paper and a subset of the data.
Common failings. Non-independence - pseudoreplication; poor randomization; bias. Suggested exercise: Discuss the the reanalysis of mouse ENCODE paper or missing data in single-cell RNA-seq paper.
From p-values to power calculation. Null and alternative hypotheses, SD vs SE, outliers, type I and type II errors, variables affecting significance, determining sample size. Suggested exercise:
Suggested exercise: Objectives, controls, experimental units (group exercise).
Afternoon Controlling variability and maximizing effect. Suggested exercise:
Genetic variability. Suggested exercise:
ANOVA, interactions, post-hoc tests, assumptions, data transformations. Suggested exercise:
Suggested exercise: Finding design faults (group exercise).
Day 2 Morning
Completely randomized, randomized block, and Latin Square designs. Suggested exercise:
Factorial designs. Suggested exercise:
Other designs. Suggested exercise:
Contingency tables. Suggested exercise:
Suggested exercise: Choosing the right design. (group exercise)
Afternoon
Good presentation of results. Summary statistics, graphs, diagrams, tables. Suggested exercise: A variation of this lesson for creating boxplots instead of bar charts.
Correlation and regression. Dealing with non-normal data. Suggested exercise:
Planning an experimental program. Suggested exercise:
Suggested exercise: Designing an experiment (group exercise).
This issue addresses which topics from should be included in a Carpentry-style lesson on experimental design. The criteria are as follows:
We will adapt a 3-day sequence of topics from the FRAME Training School. The topics are outlined here and the repository organized to reflect this outline. The rationale for teaching experimental design is described in Teaching Experimental Design. In adapting the outline we will specifically broaden its application to human studies in addition to animal studies.