What does the % of Max stand for on the Y axis of overlayed histograms?
When graphs are overlaid on the layout editor and the y-axis is left on automatic scaling, the Y-axis on the overlay histogram is “% of Max” as opposed to “# Cells or events”. If you have different numbers of events collected for the two overlaid samples, the histogram for one would be a lot taller than the other. To depict the data in a “normalized” fashion, we use % of Maximum. The % of Max is the number of cells in each bin divided by the number of cells in the bin that contains the largest number of cells. To make a histogram we take all of the events and divide them into a number of “bins” which are numerical ranges for the parameter on the X axis. Generally, FlowJo uses 256 bins, but that is specific to our program and arbitrary. The number of cells in any given bin will vary if you change the number of bins. Each graph is scaled to the percentage of its maximum bin. If it is important to compare relative numbers of events, then you may wish to have a fixed Y-axis scale. Double c
