Determining Cluster Criteria From FlowSOM/RtSNE
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8.1 years ago
CMosychuk ▴ 20

I'm somewhat new to bioinformatics and programming so please excuse me.

I used FlowSOM to cluster my data and then produced a tSNE plot from flow cytometry data using R-tSNE and ggplot2:

enter image description here

And so this is one FCS file with 8 fluorophores (I only used compensated fluoresence area data in my tSNE, no SSC or FSC). I used flowCore to generate a flowFrame directly from the FCS and so I havent done any gating in FlowJo. How would I determine what each cluster in the legend actually means? Or what phenotype they refer to?

R tSNE • 2.6k views
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