Thus, if you are dragging a Lymphocyte gate onto a sample which already has a lymphocyte gate, your options are three-fold. These options are presented to you via the node replacement dialog window.

(1) You may choose to Replace the existing gate with the version that you are dragging. Do this when you want to make the destination sample's gate the same as the one you are dragging.

(2) You may choose to Duplicate the existing gate. It will be added to the sample, but it's name will be modified by appending a version number to the name (for instance, the new gate will be named "Lymphocyte-2" in this example).

(3) You may choose to Retain the gate in the destination sample. Initially, this option may sound like it is useless, but in fact it is one of the most important features of FlowJo, so it is important to recognize how it works. With this option, FlowJo will not alter any of the gates in the destination sample; their specific versions of any particular gate will remain as they are.

If you are dragging only a single population, then the Retain option causes nothing to happen; i.e., it is not useful for this case.

But consider the case where you are dragging a whole tree of analyses: now you can use this option to add only the specific analyses or gates that the destination doesn't have, without changing the gates that already existed in the destination (because they may be slightly different than they are in the source sample). For example, let's assume that you have gated two samples for lymphocytes, but the gates are slightly different. You gave the gates the same name in each sample (Lymphocytes), because they identify the same subset of cells. In the first sample, you then generate additional gates to identify subsets of lymphocytes, like CD4 and CD8 T cells.

By clicking on the first sample's lymphocyte population while holding down the option key, you will drag the entire tree (all of the subsets below lymphocytes); this is how you duplicate all analyses quickly across samples. When you drag this whole tree to the second sample, you want only the new analyses to be added in the appropriate locations (i.e., the CD4 and CD8 gates to be attached to the existing lymphocyte gate). Here is where you would choose the "retain" option: now as FlowJo adds the dragged tree onto the sample, it will retain all of the old gates that have the same name (Lymphocytes). It then adds the CD4 and CD8 gates to this gate.

If you had chosen the Replace option, then the lymphocyte gate itself would have been changed to be identical to first one, and then the remaining nodes (CD4 and CD8 gates) would be added to it. Choose this option if you want all of the analyses and gates in both the source and the destination to be identical.

Again, the Retain option allows you to copy analyses (and populations) without changing any specific changes you made for a specific sample.

One final note: when you drag nodes to a group, then you are not presented with the dialog giving you the options. Rather, FlowJo assumes that you wish to Replace the versions of the group nodes with the ones you are dragging. This means that all samples which have the group's version of the nodes you are dragging will have their nodes updated as well. For more information, see the pages on Groups.