Hello I have been trying to run flowDensity on a flowset. The experiment is gated from an isotype control. Every flowframe will have its own isotype control flowframe. I first use degate to get the threshold on the isotype control. then i apply that threshold in the flowdensity function under gates =. This works well on a flowframe. But when i try to use it in fsApply for a flowset it does not work. The problem is that i use fsApply with degate to generate a matrix with all the thresholds for every isotype. When i put that into the gates = in the fsApply, it uses all values. I do not understand how to iterate to use the first isotype with the first sample etc. It is the isotype.thershold.fs below.

Code should be placed in three backticks as shown below

Isotype.gate.fs <- fsApply(Flowset, flowDensity, channels=c("Alexa 647-A", "V450-A"), position=c(T, NA), percentile=c(NA, NA), gates = c(isotype.threshold.fs , NA) )


sessionInfo( )