I have been gating my fcs file by using flowDensity. However- I have gotten to a point where I need to analyze closer to 10-20 fcs files. I've tried looping flowDensity with fsApply:
something like- fsApply(fs, flowdensity()) as well as fsApply(fs, Saved Flow Density Gate)
I have also tried to for loop the flowDensity parameters over the flowSet but none of this seems to work. Is there a way to gate the fcs files with the same flowDensity gate? Otherwise the flowSet is useless since i would have to parse out each single fcs file anyway. I hope this makes sense and would be happy to follow up with more information if needed.