I am trying to do clustering and dimentionnality reduction of my flow cytometry data using Spectre package. I am following their tutorial and yesterday it worked fine.
Today I increased the number of metaclusters to 20. After running for 2 hours (my data is big, by computer is old), the data table was generated, so I moved to the next step, which is subsampling to run a tsne analysis and this is where I get the error.
This is the code line that produces the error > cell.sub <-do.subsample(cell.dat, sub.targets, response.col)
where cell dat is the whole table with 27 million entries, sub targets are defined as 30 000 and response.col has Complete responders and Non responders with around 14 million points in each.
How to understand where my error comes from, especially since this script was working yesterday.
Thank you
This is the tutorial https://immunedynamics.io/spectre/simple-discovery/
