The real power of FlowJo as an analysis tool becomes immediately evident when you start to do "batch" analysis; i.e., the repeated application of set of analyses (gates, statistics, graphical outputs) to a series of samples.

Application of analyses to other samples is very easy: simply click on the analyses that you wish to duplicate, and drag them to the destination sample. You can select only a single gate (by clicking and dragging that gate), or select several independent gates (by shift-clicking and dragging any of the selected gates). In addition, you can choose to take the "children" of all of the selected gates (i.e., the entire analysis trees) by holding down the "option" key as you drag the nodes; you can also choose to take the "parent" gates by holding down the "control" key as you drag nodes. This is fully explained in another series of pages, complete with examples of these operations.

You can also apply a set of analyses to all samples within a group simultaneously. Simply drag the analyses trees onto the group. They are attached to the group itself, and then attached to each sample that belongs to the group (assuming the analysis is valid for that sample). By having these kinds of "group" analyses, you can assure that all samples are being analyzed identically. When you change a group's version of an analysis (by dragging a new version of a gate onto the group), then all samples belonging to the group will be automatically updated with the new copy (with the exception of those samples which have "special" versions of such gates). These operations are fully explained in the pages on group analyses.

Another kind of batch analysis is the extraction of statistical information from a series of samples. This is accomplished through the table editor. Using the table editor, you specify what sorts of statistical information you wish to collect for each sample. Then you create the table for the current group; FlowJo allows you to either save the table to a file (which you can export into a spreadsheet), to the clipboard (so you can copy it directly into a spreadsheet), or print it out. Table definitions are saved with the workspace so that you can use them again in the future.

The final type of batch analysis is the extraction of graphical displays for a series of samples. For this, you use the layout editor. The layout editor allows you to arrange several graphs however you wish. This graphical layout is then applied to the series of samples in the current group; the result can be saved to a disk file (PICT format), copied into other applications (like Canvas), or printed.

Because FlowJo saves all of this information in the workspace, it is a simple matter to read new samples into the same workspace and apply the same batch analyses to those samples (typically, this is accomplished by dragging the new samples into the appropriate groups; and then applying a table or layout to those groups).

 See Also:  Groups, Layout Manager, Table Editor