Hi there,
This is likely a beginner's question, but I failed to find an answer to it here.
I would like to calculate the F measure to compare cell populations derived via different gating approaches (e.g. manual vs automated; or manually gated by two different people), similar to what was done in the FlowCAP challenge (https://www.nature.com/articles/nmeth.2365).
Maybe there is an easy solution, but my initial idea was to create intersections between the flowFrames of a manually and automated gated specific cell population in order to determine my true positive and false negative subsets - this should be all I need to calculate the F measure as i already know the rest. I could not find out how to achieve this easily, i.e. create an intersection of two flowFrames in one step. Do I have to create a filter list to which I add all gate filters of the gating tree leading to my automatically gated population of interest (e.g. root->debris->singlets->lympho->cd3) and then apply this filter list to the manually gated population (e.g. cd3) to get the intersecting subset?
Any help with this is appreciated.
Cheers, Stefan
Hi Stefan,
You should also read (at least) those two articles: https://onlinelibrary.wiley.com/doi/full/10.1002/cyto.a.23030 https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1738-8
There is a lot of R code in the repository of Lukas, and of course, fro computing F-measure https://github.com/lmweber/cytometry-clustering-comparison
Best, Samuel
Moved comment to answer