Copying Gates
Copying analyses (gates, statistics, kinetics, cell cycle, etc.) from one sample to another is very easy: simply click on the analysis (a gate, statistic, or population node), and drag it to the destination. The node is added on to the destination node as a "child" of the destination (i.e., it is applied to only those cells which fall within the population you drop the analysis on).
You can drag entire trees around this way, selecting children, parents, or multiple nodes. There are specific rules for how these are taken around when you drag; see the pages on dragging and dropping.
Note that if you drag a subpopulation onto a population which already has a subpopulation with the same name as that you are copying, then FlowJo asks what you would like to do: you can replace the existing subpopulation, you can retain the existing subpopulation, or you can add the current subpopulation with a change in its name. (The reason for all of this is that FlowJo does not allow you to have two subpopulations with the same name at the same level of analysis). These options are more fully described in the pages on replacing nodes.
You can automate the process of applying analyses to samples by using groups. You can add analyses to a group; then every sample which belongs to the group or is later added to the group gets those analyses. This is one of the powerful batch analysis features of FlowJo. You may view an example of group-based analysis.
You can drag analyses across workspaces; in other words, you can drag an analysis node from one workspace and drop it onto a sample or a group in a different workspace. You need to have both workspace windows open to do this; simply drag from one to the other.