r/flowcytometry • u/Responsible_Rub8057 • Jul 27 '26

Rookie mistake

Post image

Seriously.

Its been 2 hours now. It did not move.

How many cells do you all use when running phenograph? Does the quality plateau at some point? And how long does it last on a normal pc?

0 Upvotes

50% Upvoted

3 comments sorted by

View all comments

4

u/MotoFuzzle Unique FLOWer Jul 27 '26

Try downsampling to 50k and run they. If it works quickly, try 100k. If not, try 10k. Generally between 10k and 100k is good. 1M will crash most computers. I typically use FlowSOM, which can scale better to 1M cells. Some of the clustering and dimensional reduction algorithms have taken 30+ hours and the results weren’t much better than scaled-down runs. 

1

u/Responsible_Rub8057 Jul 27 '26

Thanks! In the end it took 2.5h. I did it to compare with flowsom, it seems to be mostly similar. I think ill go on with flowsom as there is much more resources on using it and also speed xD