Statistical Inference for Biology

The Jackson Laboratory

Online

May 16, 19, 23 & 26, 2022

1 - 4pm EDT (5 - 8pm UTC)

Instructors: Fernando Cervantes Sanchez, Rohit Goswami, Ahmed Sadeque, Sue McClatchy

Helpers: Tayaza Fadason, Olaitan Awe, Neil Kindlon

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General Information

More data are better than less data, right? When interpreted through sophisticated analytical skills the answer could be yes. This lesson presents statistical skills and knowledge to help data analysts in the life sciences to avoid some of the most common pitfalls of big data. Lesson material is derived from the HarvardX Biomedical Data Science series, part of which is published as the book Data Analysis for the Life Sciences (Irizarry & Love, 2016).

This is a pilot workshop, testing out a lesson that is still under development. The lesson authors would appreciate any feedback you can give them about the lesson content and suggestions for how it could be further improved.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: May 16, 19, 23 & 26, 2022. Add to your Google Calendar.

Requirements: Participants must have access to a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.). They should have a few specific software packages installed (listed below).

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email susan.mcclatchy@jax.org for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Who can attend?: The course is aimed at graduate students and other researchers at JAX and elsewhere. You should have basic R skills to participate successfully in this workshop.

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Schedule

Monday, May 16

1:00	Overview and introductions
1:15	Inference
2:45	Coffee/tea break
3:00	Populations, Samples and Estimates
3:55	Wrap-up
4:00	END

Thursday, May 19

1:00	Central Limit Theorem and the t-distribution
1:50	Central Limit Theorem in practice
2:45	Coffee/tea break
3:00	t-tests in practice
3:55	Wrap-up
4:00	END

Monday, May 23

1:00	Confidence Intervals
2:45	Coffee/tea break
3:00	Power Calculations
3:55	Wrap-up
4:00	END

Thursday, May 26

1:00	Association tests
2:45	Coffee/tea break
3:00	Permutations
3:45	Wrap-up
3:50	Post-workshop Survey
4:00	END

The lesson taught in this workshop is being piloted and a precise schedule is yet to be established. The workshop will include regular breaks. Please contact the workshop organisers if you would like more information about the planned schedule.

Setup

To participate in a workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

Two monitors: If you have two monitors, plan to have the tool you are learning up on one monitor and the video conferencing software on the other.
Two devices: If you don't have two monitors, do you have another device (tablet, smartphone) with a medium to large sized screen? If so, try using the smaller device as your video conference connection and your larger device (laptop or desktop) to follow along with the tool you will be learning about.
Divide your screen: If you only have one device and one screen, practice having two windows (the video conference program and one of the tools you will be using at the workshop) open together. How can you best fit both on your screen? Will it work better for you to toggle between them using a keyboard shortcut? Try it out in advance to decide what will work best for you.

This blog post includes detailed information on how to set up your screen to follow along during the workshop.

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

Video Tutorial

Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.

Video Tutorial

Instructions for R installation on various Linux platforms (debian, fedora, redhat, and ubuntu) can be found at <https://cran.r-project.org/bin/linux/>. These will instruct you to use your package manager (e.g. for Fedora run sudo dnf install R and for Debian/Ubuntu, add a ppa repository and then run sudo apt-get install r-base). Also, please install the RStudio IDE.