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Table of Contents

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

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In FlowJo, after importing your cytometry data, click the 'Check sample quality' button in the tools workspace. This will flag 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 in FlowJo

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• Have R installed (version >3.4)
• Install BioConductor
  • source("https://bioconductor.org/biocLite.R")
  • biocLite("flowCore")
  • biocLite("flowClean")
• Have FlowJo installed with the correct R path in the preferences
  
• If not already present, download and move FlowClean.jar file into the FlowJo plugins folder (available from the FlowJo exchange)
• Restart FlowJo
• Select sample and navigate to Plugins, FlowClean. Select parameters and compute. Example output is shown below.
  

Reading FCS files in RStudio

1. Open RStudio

2. Install Bioconductor

   Code Block
   firstline ## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite() title Install Bioconductor
   ## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite()

   
   

3. Set the FCS folder as a variable

   Code Block
   fcsfolder<-system.file("extdata",package="fcsdata")

   
   

4. Still in progress...