The graph specifications control what metric is used on the Y-axis, and whether smoothing will be applied. When you click the Options disclosure triangle in the kinetics window, the options shown below appear. They modify the attributes of the current graph (or currently-selected gate.)   The ‘Statistic’ selection is the statistics that will be applied to… Read more »

FCS Scan provides an interface for locating FCS files from local or remote file systems and generating Workspaces from files located.  In situations where your IT department moves whole directories, or you can’t remember where you stored a sample set it can really come in handy. This tool is also extremely useful for finding files… Read more »

Data can be exported from the kinetics platform to the layout editor, the table editor, or as binned data. Exporting graphics to the layout editor Like any other node in FlowJo, the kinetics node can be dragged to the layout editor to create a graphic.  As you can see in the graphic below, the model… Read more »

FlowJo allows you to add new parameters to your data. These parameters behave like parameters that were collected: you can display them, calculate statistics on them, etc. It is important to note that although newly derived parameters are not added to the original data file, they can become part of a new data file if… Read more »

FlowJo allows you to add new parameters to your data by performing operations on existing parameters. The most common operation includes the creation of ratio parameters. This tool will also apply a Gain or Offset to an existing parameter and set the range for scale values. To learn about each of the parameter types, click… Read more »

FlowJo allows you to add new parameters to your data by performing operations on existing parameters. We call these “Derived Parameters“. Once created, they behave like parameters that were collected at acquisition. They can be used in the graph window, or in plots within the layout editor. To open the Derived Parameters interface, click the… Read more »

A more detailed explanation of the algorithms in the Population Comparison platform FlowJo’s comparison platforms support four different comparison algorithms. Two algorithms (Overton and SED) are used to calculate the percentage of positive cells found in the sample (not in the control). Two algorithms (Kolmogorov-Smirnov and Probability Binning) are used to determine the statistical difference between… Read more »

Probability binning is the algorithm used for partitioning data for the Chi Square test. For the Probability Binning (PB) algorithm, the distribution is divided into a number of bins of the same height. The number of events falling into each of these bins is compared between a test and a control sample, and a Chi Squared-like… Read more »

T(x) is shorthand for the Chi-square difference.  It is the metric used to assess differences in samples that have been binned using Probability Binning. T(X) is a statistic which provides an indication of the probability with which two distributions are different and also provides a metric by which multiple distributions can be ranked.  T(x) is… Read more »

Tips for Using Population Comparison. In FlowJo, the Population Comparison platform is used to compare single or multiple parameters from a test sample to a single control sample OR a composite of more than one control sample.  The control population is a different population (either another sample or another population within the same sample) with which the test… Read more »