Naming Nodes
FlowJo identifies populations (samples, or gated subsets of samples) by a name that you assign. Naming populations is very important for the way in which FlowJo works... especially for batch operations. The rules for naming gates are similar to what we expect for rules for naming people in families: siblings cannot have the same name; however, different generations can have gates with the same name.
When you specify a kind of analysis (for instance, a statistical measurement, or a gate selecting a subset of cells), it is applied to a population. During batch operations, you can specify that this analysis be applied to all samples within a group. FlowJo decides how to do this by looking at the names of the gates.
For instance, you may have 3 samples in a workspace. You first decide on a gate to exclude dead cells and clumps of cells; you apply this gate to a group containing all three samples (and call it "Live cells"). After looking at the 3 samples, you find that you have to alter the position of the gate slightly for each one--therefore, the gates are no longer identical.
Now you create a statistic that tells you the median forward scatter signal for "Live cells." Thus, you create a new node (analysis) attached to the "Live cells" gate of the first sample. When you now drop this node on the group's version of "Live cells", the node is attached to each sample's version of its own "Live cells" gate. Even though each gate is slightly different, FlowJo assumes that the gate represents the same population and thus you want the same operations applied to that gate.
This is why a gate cannot have the same name as another gate of the same population: FlowJo would not be able to decide which gate you want analyses applied to. Note that FlowJo decides which gate you mean by not only name, but generation. Thus, if you have a sample which has a "Live Cells" gate as a child of a gate you named "Lymphocytes", this is NOT the same gate as "Live Cells" attached directly to the sample--and, in the example above, would not have your statistical analysis applied.
Realize that the complete name of any population is actually the concatenation of all of its ancestors' names with its own name. Thus, in a sample, if you have created a lymphocyte gate, and within that a CD3 gate, then that subpopulations "true" name is "Lymphocyte/CD3". FlowJo only shows you the "CD3" portion of the name, as the "Lymphocyte" portion is implied by the indentation in the workspace. You could subset the "CD3" population and also call it CD3. This is legal, because its full name would be "Lymphocyte/CD3/CD3" which is distinct from "Lymphocyte/CD3". However, it could be confusing--so try to avoid duplicate gate names at any level.
If you wish, you may get help on how to create new subpopulations by gating.