Overview

This is the first of the three workshops which are specific to the Immunobiology strand. The aim of these workshops is to teach you how to analyse the flow cytometry data you will collect in the practicals. In this workshop, we will guide you through the analysis of a sample data set just like the one you will generate. Jillian collected these data in designing this set of practicals. You will learn both how to analyse the data and what your own data should look like.

Learning objectives

The successful student will be able to:

  • explain what is in a flow cytometry data set

  • import fcs files, explain a “flowFrame” and a “flowSet” and access the column names and data in them

  • apply automated quality control to a flowSet with the flowAI package

  • explain why we use the “logicle” transformation and apply it to appropriate channels

  • cast the data into a dataframe to use standard tools for filtering, summarising and plotting data

  • explain the purpose of gating and apply appropriate gates to flow cytometry data

  • create appropriate summary statistics and figures to demonstrate the results of the analysis

Instructions

  1. Prepare

    1. 📖 Read what the sample data are, what analysis is needed and what tools we will use.

  2. Workshop

    i.💻 Analyse the sample data set.

  3. Consolidate

    1. 💻 Set up your RStudio Project for the analysis of your own data.