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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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Specific workflows when dealing with data generated at WRHFlow
Please note I am no expert in R/RStudio and apologise in advance if my nomenclature or the below has errors.This is still under construction so please email me and we can update this guide ASAP.
| Method | Useful for... | How to | Example image |
|---|---|---|---|
| tSNE - R | |||
| tSNE - FlowJo | |||
| tSNE - MATLAB | |||
| SPADE - R | |||
| SPADE - FlowJo | |||
| SPADE - MATLAB | |||
| Scaffold | |||
| Vortex | |||
| FlowClust | |||
| FlowSOM | |||
| CITRUS | |||
Workflow 1 - Analysing a high parameter single FCS file.
This workflow will demonstrate tSNE, SPADE, Scaffold, FlowClust, FlowSOM, VORTEX.
Workflow 2 - Comparing group A to group B
This workflow will demonstrate comparison of samples.