This page has been archived and further updates will be on Christopher’s GitHub page.

R flow cytometry course

The files and presentation from the Cytometry Core Facility flow cytometry data analysis course in R by Christopher Hall.

This is the the R course I have designed to help bridge the gap between the wet lab flow cytometrist and the bioinformatician. It is not designed as a full R course, or a full flow cytometry data analysis course. It is intended to open the non-programmers eyes to the world of data analysis in R.

The course is designed to be three hours long.

Contents

1. PDF handout: Basic R and flow cytometry data analysis in R
2. R files to save typing -- "R handout.R" and "Your data.R"
3. Example FCS files: 4 files of 8 peak beads and 1 file of lymphocytes stained with 6 colours

Instructions

Download the fcs files, read the PDF handout, and use the included scripts.

Feedback

Let me know what you think by email, raising an issue, or through Twitter

Info and help

Remember that the code here is an amalgamation of all the help files from the flow cytometry R packages. If you are stuck then check the documentation. Either use the ? R command or check the Bioconductor package page:

flowCore

flowWorkspace

openCyto

flowAI

To do list for next time

• Use more data and analyse the titration experiment
• Add comparative statistics
• More clustering examples