Tutorial on tSNE and FlowSOM Step-by-Step tool usage in FlowJo V10 

I think the safest way is to concatenate on everything, otherwise you'd lose any statistical power. You'd effectively only have n=1 per group. However, that being said, this workflow starts to become pretty impractical when you have so many samples! It's one of the main downfalls I've seen. For example, let's say you wanted 100,000 total events to run tSNE. If you concatenated all, then you'd only have 4,000 cells per sample - a very small number to figure out population frequencies from each sample, especially if you're trying to gate rare populations. If you do separate tSNE runs on separate samples, the same cell populations wont necessarily plot to the same places on the map, thus, you couldnt compare the tSNE maps to each other. I'd try concatenating a much larger number of cells so you make sure you're getting an acceptable number per sample and running tSNE on everything. But it may take a really long time to run...

Hi, did you succeed in doing this cross samples comparison? thanks

Yes!! I did complete it!! And I did it as suggested 😊

@@Mariiamdov Thanks. So did you merge the 25 mice into one sample and separated them by the "sample ID" keyword?

Great question! I have a similar problem but with 51 samples. how did you separate your samples on the plot after concatenation?

Great question.. wouldlove to know this too

I have the same question!

Thank you for this question. Ideally you would be able to do exactly this and it would make your life easier and your data more robust. However, I have never been able to do it in practice. If you try to drag the flowSOM gates onto the original files it will tell you there is a missing parameter and not allow it. If you try and run flowSOM on one of the original files and select "Apply on map" for the flowSOM map generated on the concatenated file, the execution halts in R for an unknown reason to me. So if anyone can figure this out it would help me as well!

have you found a solution to this yet? @@ucmercedscifstemcellinstru711 loved your tutorial and found it very useful!

right click on thr graph and go to properties, then unclick hide axes/labels/numbers etc. Hopefully you found this already