Sometimes when I drag gates, their frequencies don't show up in the workspace, other times they do. Why? How do I get the frequency when it's not there?

FlowJo's mode of calculation is what is called "lazy": it only recalculates gate and statistics when it is absolutely necessary (for instance, to create a graph, table, or layout). It also computes gates or statistics immediately if the file is in memory. For files which haven't been read in yet, or were dumped from memory to make room for other data files, these gates will not be computed until they are necessary to complete other operations. Displaying the frequencies in the workspace is considered a low priority. If FlowJo were to automatically recalculate everything as soon as you drag and drop the gates, then it could take a long time before you could do something else (for instance, dropping a tree of 30 gates and statistics onto a group of 100 samples!).

Nonetheless, you can force FlowJo to immediately calculate gates and statistics. Simply select the node(s) you wanted updated, and select "Recalculate" (cmd-"="). FlowJo computes the statistics for the nodes you have selected (and any of their children). You can also select a group (or group analysis node), and then the recalculate command forces all samples to recompute.

You can also select a preference that specifies whether recomputations should always occur instantly, only if the sample is loaded in memory, or only when need by the Table Editor or Layout Editor.

Note that a gate or statistic does not have to be presently computed in order for a table or layout to function properly. Tables and layouts will force the recomputation if necessary.

My workspace window is very cluttered with gates and analyses-it takes me forever to scroll to the sample I want. How can I clean it up all at once?

Select all samples (cmd-A), and while pressing the command key, click on a triangle next to a sample node. This will close up that sample-and pressing the command key asks FlowJo to close up all other nodes at the same level.

I created table. I got one row for each sample, but I got multiple identical columns with identical values.

Only drag any particular statistic into the table a single time from any sample. FlowJo creates one column for every statistic that you drag into a table. So if you drag the same statistic from three different samples into the table, then each one of those three will be applied to all samples--resulting in three identical columns in the output.

How can I copy layouts or tables from one workspace to another?

You can't. We are still thinking about how to do this, and hope to have this functional in version 3.0.

I am trying to select a gate that is entirely underneath another gate, but when I click I just select the top-most gate.

Press the command-key while clicking to select gates: this will iterate through all gates in the same area as the mouse, each time selecting the next-lower one.  This also works in the Layout Editor to select "hidden" items.

In my Layout Editor, I don't have "Placeholders" selected, yet I get a placeholder for a graphic.  When I generate the batch output, I don't see any graphs for that item.

There are a couple of reasons that you might see a Placeholder for a graphic.  If Iteration is "Off" and you see a Placeholder, then most likely the original sample that you dragged into the layout editor was deleted.  If Iteration is set to a particular value, then most likely FlowJo could not identify a corresponding graphic as was demanded by the Layout Editor for the current iteration value.  Note that, by default, FlowJo requires you to match parameters AND stains in order to create a graphic (i.e., each sample must have the same parameters such as "P1", "P2", etc., that are being displayed), and the same reagent on each parameter (such as "CD3", "CD45", etc.).  The latter constraint can be relieved by selecting the appropriate Preference under the Tables & Layouts Preferences.