The key to unlocking the power of groups comes down to a few simple rules. File annotation is critical. When it comes to utilizing groups for batch operations, nothing is more helpful than using keywords in your data. If you didn’t annotate during acquisition, you can always generate a keywords series or a value series in FlowJo to help get patterns in… Read more »
Groups Example
This example of group operations uses an experiment in which 18 samples of human PBMC were stained with two combinations of antibodies, collected over a series of days. How might this data be organized? The stain combinations are listed by panel in the table below. Panel . APC-Ax700 . APC-H7 . APC-Ax647… Read more »
Creating and Editing Groups
When you click the Create Group button (under the FlowJo tab or in the static toolbar) you are presented with the dialog window below. This window also appears when you double-click on a group in order to edit the criteria for membership. Overview: The basic process for creating a group is to: Give the Group… Read more »
Deleting Group Nodes
Gates or statistics that have been added to a group must be deleted from the group. If you select a group owned gate or statistic from the group analysis pane in the top half of the Workspace, and click ‘Delete’ on your keyboard you will see a confirmation dialog with four choices: The outcomes from selecting each are:… Read more »
How to Apply Gates and Statistics to a Group
Did you make a gate on one file that you would like to apply to an entire group of files? Just drag and drop the gate to the group, then! FlowJo is designed to allow the user to analyze entire experiments, as opposed to individual samples. The general plan throughout FlowJo is to define what… Read more »
Find / Replace tool
The Find / Replace tool is a fast approach to correcting keyword errors and omissions. FlowJo’s power truly comes down to batch analysis, and batch analysis relies heavily on keyword annotation. Without proper labels in keywords, analysis can become error prone due to manual iteration through dozens/hundreds of samples. One way to reconcile keyword value variations is through… Read more »
Accepted File Types
You have probably figured out that FlowJo can open FCS files from all flavors of instrument manufacturers (link). But, you may not realize that FlowJo can open a wide variety of file types for analysis, meta data, or preference related options. Here are the file types recognized by the Workspace: ACS files ACS (Archival Cytometry… Read more »
FCS Keyword List
Keywords are paired combinations of a category and a value that pertain to the cytometric data contained in a workspace. Keyword values can either be imparted to the FCS data file at the time of collection, or added post-acquisition in FlowJo. In either case they are accessible through FlowJo, and are useful for organizing data. FCS… Read more »
FlowJo and FCS Files
FlowJo accepts FCS and LMD (embedded fcs format) files from nearly all cytometers. To load your files into FlowJo, drag-and-drop a folder of files onto the Workspace window, or click the Add Sample button to get a file navigation window, browse to your folder of files and click Choose. Note that FlowJo will automatically create… Read more »
Export or Concatenate Sample Data
Exporting data from FlowJo is helpful for a variety of tasks. For example, you may need to create a new FCS file by merging multiple files together (concatenate) to facilitate rare event analysis, or export CSV files that include your workspace structure (gating tree and columns) for use in a downstream application. The following section describes how to export data as… Read more »