There is a youtube video by FlowJo titled 'Concatenation and tSNE in FlowJo Webinar'. In it, they use a test data with multiple groups and multiple samples per groups. It can serve a basis for your analysis.

Thank you Wilfred!

HI Roberta,

You can find simple instruction here: http://docs.flowjo.com/d2/advanced-features/dimensionality-reduction/tsne/