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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")
  Install flowCore (copy and paste the following)& flowCore
  • source("https://bioconductor.org/biocLite.R")
  • biocLite("flowCore")
• Install PNG package
  • install.packages("png")
• Install flowAI
  • source("https://bioconductor.org/biocLite.R")
  • biocLite("flowAI")
• Install stringi (I required this package additionally)
  • biocLite("stringi")
• Have FlowJo installed with the correct R path in the preferences
  Image Added
• Download and move FlowAI.jar file into the FlowJo plugins folder (available from the FlowJo exchange)
• Restart FlowJo
• Select sample and navigate to Plugins, FlowAI. Select parameters and compute. Example output is shown below.
  
  

Active sample quality check - FlowClean

To enable FlowClean

• Have R installed (version >3.4)
• Install BioConductor
  • source("https://bioconductor.org/biocLite.R"
  • biocLite("flowCore")
  • biocLite("stringiflowClean")
• Have FlowJo installed with the correct R path in the preferences
  
• Download and move FlowAIFlowClean.jar file into the FlowJo plugins folder (available from the FlowJo exchange)
• Restart FlowJo
• Select sample and navigate to Plugins, FlowAIFlowClean. Select parameters and compute. Example output is shown below.
  

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Active sample quality check - R

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