search

lmweber / diffcyt

R package for differential discovery analyses in high-dimensional cytometry data
MIT License
19 stars 12 forks source link

Integration w/ FCS Express #42

Closed tdfy closed 2 years ago

tdfy commented 2 years ago

Hello,

I am new to flow cytometry analysis and supporting a group remotely. The team prefers to use FCS Express for HD clustering and has little command line experience. I understand FCS Express utilizes FlowSOM, as does diffcyt, and also allows for integration of R scripts. I was wondering if you could advise on how to perform DA/DS within this FCS express environment (Windows) provided metadata/design-contrast matrices would be imported by diffcyt R script? I suppose the alternative would be to have the group export the annotated fcs files (assigned clusters) and execute the script (non-wrapper) in a Command Prompt.Thanks!

-Todd

tdfy commented 2 years ago

I ended up wrapping diffcyt functions in the R parameter transformation tool

https://fcsexpressdownloads.s3.amazonaws.com/manual/manual_IVD/index.html?r_add_parameters.htm