There is a special case group:  the "All Samples" group. It contains (by definition) all of the samples known to the workspace. The "All Samples" group can neither be renamed nor deleted.

You can add other samples in the workspace to any group. Just click on the sample and drag it to the group. To remove a sample from a group, select the group, then select the sample and press the delete key. If the current group is "All Groups" and you delete the sample, then you will be permanently removing the sample from the workspace.

There is one unbreakable rule with regards to groups: Every sample belonging to a group must contain every analysis that the group specifies. Of course, if the group specifies analyses that are not applicable to the sample, then this doesn't happen. (For example, if you have created a gate based on compensated parameters, and a sample that is not compensated is added to the group, then those gates cannot be added to that sample. Once you compensate the sample, however, the gates will be automatically added.)

If a sample belongs to multiple groups, then it will have all of the analyses from all of the groups it belongs to. Whenever you add a sample to a group (by dragging into the group), that group's analyses are automatically added to the sample.

Associated with group names is a color and text style. Any gate that was attached to a sample through a group operation is given the same color and style as the group that originated that gate. Therefore, any gate within a sample that has the group's color and style is guaranteed to be identical to the group's version of that gate. When you change a group's version of a gate (by dragging a new version of that gate onto the group), then all samples with the group's version of the gate are likewise updated.

If you modify a sample's version of a group's gate (for instance, if you decide that a lymphocyte gate for one sample should be slightly different and you move it), then that gate will now appear in the workspace window in black and plain text (unlike the group's gates). This is how you can tell when a gate has been modified.

Note that modified gates will still behave in other ways like group gates: when you attach a subpopulation to a group's gate, it will be attached to the same gate in all samples, whether or not they are identical to the group's version of the gate.

If you have modified a gate and decide later that it should be identical to the group's version, you can select the gate and choose the "Unify gates..." option under the "Experiment" menu. Likewise, if you select a group's gate and choose thise menu option, then all sample's versions of this gate are made identical to the group's version.

How do you know what the group's version of a gate looks like? Simply open any sample which has the group's version of the gate (i.e., the node is displayed in the color and text style of the group). If you change this sample's gate (move it), then you are only changing that sample's version. To change the group's version, drag the node back onto the group after you have made the modification­the update happens automatically. (Again, only samples which have the group's version of this gate will be updated­if they have their own, modified, version, they will remain untouched).

If a sample belongs to multiple groups which all have an analysis of the same name, then the sample's version of the gate will be whichever it got first.

Deleting nodes associated with groups have special consequences:

• If you delete the node in the group itself, then it is removed from the group. You are then asked if you want to remove the same nodes from all of the samples; if you choose not to remove them from the samples, they are left alone (but they are then owned by the samples­i.e., drawn in black and plain text­since they no longer belong to a group).
• You cannot delete a sample's node which is identical to the group's node, since every sample must have every analysis belonging to the groups that it is in.
• If you delete a node which is a modified version of the group's node, then FlowJo will replace it with the original, group's version of the node.
• If you delete a sample from a group, then it is removed from the group and all analyses which come from the group are left with the sample (but reassigned to be owned by the sample, not the group).
• If you delete a group, then all of the group analyses nodes are assigned to the samples.

If you rename a sample's version of a group node, then a copy of that node is made with the new name, and the sample will retain a node with the same name as the group's node.