To calculate additional statistical information about your subpopulations, you can add statistics to the subsets. Select the population, then the Signma button from the workspace tab. The definitions for available statistics are here. Once a statistic has been added to a population, its definition can be copied to any other population or group of samples via… Read more »

Quadrant gates split a population into four adjacent, discrete subpopulations. The gates are labeled starting at the top left and proceeding clockwise.  The double positive population is always Q2, and the double negative is always Q4.  Q1, Q3 are the single positives. Drawing Quadrant Gates Select the quadrant tool from the gating tool pallete in the graph… Read more »

Begin data analysis in FlowJo with the user- friendly Graph Window. Quickly gate, navigate, and add statistics to your populations using FlowJo’s intuitive menu bars and icons. Data analysis in FlowJo begins with the Graph Window. The Graph Window provides an interface to begin gating your populations, adding statistics, and is the first step in creating… Read more »

In this example, we will use graph window movies to visualize 3 dimensions of data on a subset of cells. A general overview discussing generating a Graph Window Movie can be found here. In this example, we will examine whether two murine CD8 T cell costimulatory molecules (CD27 & CD28) are upregulated early after virus infection… Read more »

Movies are an ideal way to visualize changes in the fluorescence intensity of various markers or examine the changes in data during acquisition (e.g. by time). They are also a powerful way to show changes or trends in populations across an entire data set in a compact format. They can be added to any presentation… Read more »

The Graph Window is at the heart of data analysis. FlowJo vX has incorporated several menu options to ease the export, analysis, printing, saving, and overall functionality of the Graph Window. The Graph Window menus in the red box are explained below. The File menu: Close: Closes the active graph window. Close All Graph Windows: Closes… Read more »

FlowJo v10 makes it easy to convert bivariate dot plots to univariate histograms with a click of a button! To view your plot as a histogram, simply click the drop-down menu on the left side of the Graph Window and select “Histogram” from the menu. Use histograms to view frequency distribution of your flow data,… Read more »

Bivariate density plots are computed the same way as contour plots (equal probability contouring). This algorithm generally generates graphs which are most accurately interpreted by our brains, in terms of relative frequencies of sub-populations. While all contouring algorithms have pros and cons, probability contours have the fewest disadvantages. There are a couple extra options found… Read more »

The Graph Window is the analysis interface that facilitates data visualization and gating. FlowJo’s Gating tools are powerful instruments that help you get the most out of your FACS data.  Gating Defined Gating refers to the process of selecting a subset of the collected events for further analysis. Subsets can continue to be gated to generate… Read more »

Gating is the process of selecting a subset of collected events for further analysis. Naming these populations and subpopulations is critical to keep your analysis organized. Naming a New Gate After you have completed drawing a gate using the gating tools in the graph window, you will be prompted to name the subset. FlowJo generates a name… Read more »