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The table editor is the means by which you can
generate a series of statistical calculations for all samples in
a group. These statistics can be any of the statistics FlowJo calculates:
medians, frequencies, etc. In order to generate a table, you will
first have to generate the statistics you wish to export on at least
one sample. To create a table, you should open the table editor. This can be done in one of two ways: either click on the table editor button in the workspace window, or select the table window from the Windows menu (command-T). This will bring up the table view window, from which you can easily create previously-defined table outputs (see right). From the table view window, you can switch to the Table Editor by clicking on the Edit button. This brings up the table view window, from which you can activate the table editor window. You can switch back to the tabel view window by clicking on the Edit button again.
 Use
the table editor to define a new table definition. A table definition
is not the output data itself. Instead it is the specification
of what columns the table will contain, when it is generated.
You can have as many table definitions in the workspace as you wish.
You can create new empty definitions, duplicate existing ones, or
delete them using the button in the top left corner of the window.
To add statistics to a table definition, simply click on them in the workspace window and drag them to the definition pane on the right hand side of the table editor window. (You can use the control and option keys to modify whether or not you want to take all the parents or children, respectively; for more information, see the pages about dragging and dropping nodes.) When you drag a population node into the table editor, it assumes that you want the frequency for that gate as the statistic. To add new statistics to a table, just click on them in the workspace window, and drag then into the editor window (the rightmost window in the table editor shown immediately above). Each row in the this window corresponds to a column which will be created in the output table; you can change the order of these columns by clicking and dragging the statistics around. The table is created for those samples in the currently-selected group: remember to click on the appropriate group in the workspace window before you create the table! Only drag statistics from a single sample into the table (the table editor will automatically generate these statistics for each sample in the group). Tables are templates: when you apply or create a table, each row in the table is applied to every sample in the current group--irrespective of which node you actually dragged into the table. Each different table definition in the table editor is a different template. When you create a table, FlowJo will cycle through all of the samples in the currently-selected group. For each analysis that you have dragged into the table definition, it searches for the same population in each sample. If the population does not exist, then it leaves a blank for that entry. (For instance, if the statistic you copied was the median FITC fluorescence of a "Lymphocyte" gate, and the "Lymphocyte" gate does not exist in all samples, then those samples will have blank values for this statistic). Therefore, the statistics are only gathered for those samples which have the appropriate gates already applied to them. However, there is no need for all samples to have the statistics nodes already applied to them; FlowJo will calculate the appropriate statistic whether or not you have added that node to the gate already. (Again, it must be stressed that the gates DO have to be applied to the sample).
Column Names. In the output file, the first line has a tab-delimited list of column names. Each column name is a concatenation of the full name of the population (including all "parents") and the statistic name itself. For example, "Lymphocytes/CD4:Freq. of Parent" would be the name for the column with the frequencies of CD4 cells within the Lymphocyte gate. These names can become unwieldy in length... you might want to keep your subset names as short as possible. In addition, you can have FlowJo export abbreviated statistic names (in the example above, "Freq. of Parent" would be replaced by "%P"). You can set this preference in the Preferences for Tables & Layouts. |
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Finally,
you can choose the resulting table to be saved to a disk file, copied
to the clipboard. Saving to a disk file is probably the best choice;
you can then import the data into a spreadsheet. Any spreadsheet
should be able to import the data; specify that the first row of
the table has the column headers. The resulting table has one row
for every sample in the group; each column is the statistic that
you have dragged into the table template editor.
Keywords.
The table editor also supports including sample file keywords.
A keyword is any attribute listed in the text section of
the FCS file. Above the list of columns is a button with a
picture of a key on it. Press this button to bring up a dialog
which will allow you to select the keyword(s) to be included in
the table. You can use shift- and command- clicking to selection
multiple items from the list, if you wish to include more that one
keyword into the table at a time. Keywords are appended to
the table definition. Drag the icons up and down within the
list to reorder.