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Cytometry Data Analysis

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This page is currently under construction - check back soon!


Workflows


AlgorithmVisuallyIdentification
Example output
Data pre-processing




Novel population discovery




What is different and of interest?




Time course




Alignment of data




Single cell RNA sequencing




Step by step

Getting started for advanced flow cytometry data analysis

Software that we may utilise in different workflows (or access ARGUS for a desktop pre-installed with software)

  1. Download and install R (latest stable version, or a specific version if needed) from here - https://www.r-project.org/
  2. Download and install RStudio Desktop from here - https://www.rstudio.com/products/rstudio/#Desktop
  3. Download and install FlowJo from here (and organise a licence if you haven't already got one)
  4. Download and install SeqGeq from here (and organise a licence if you haven't already got one)
  5. Download and install Matlab

Data pre-processing


FlowJo Check Sample Quality

In FlowJo, after importing your cytometry data, click the 'Check sample quality' button in the tools work space. This will identify any samples that should be checked. FlowJo plots the median values for each parameter over time and flags any that are outside of 2 standard deviations. Green is good. Any thing else should be reviewed. 


Active sample quality check - FlowAI

FlowJo also provides access to 2 active cytometry data quality plugins. FlowClean & FlowAI

To enable FlowAI

  • Have R installed (version >3.4)
  • Install BioConductor
  • Install flowCore (copy and paste the following)
    • source("https://bioconductor.org/biocLite.R")
    • biocLite("flowCore")
  • Install PNG package
    • install.packages("png")
  • Install flowAI
    • source("https://bioconductor.org/biocLite.R")
    • biocLite("flowAI")
  • Have FlowJo installed with the correct R path in the preferences
  • Download and locate FlowAI.jar file into the FlowJo plugins folder. 
  • Restart FlowJo
  • Select sample and navigate to Plugins, FlowAI.

Active sample quality check - FlowClean

Active sample quality check - R

Data transformation explained





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