The cells that were squished against the axis on the top plots are now off of the axis and are shown as clusters of cells and it is now clear that the data is properly compensated. The plots at the bottom have the display transformation applied. It is worth noting that the cells against the axis are much more obvious on the contour plot. The top plots are the normal display and there are a large number of cells against the x-axis. Is shown as the horizontal line on each plot. All the plots show the data properly compensated. On the left two plots, the data is displayed using 5% contour plots with outliers on the right, pseudocolor plots. The four data plots in the figure below all show the same data. Note that the data is exactly the same, but FlowJo's display transform allows you to view the negative populations as nice symmetrical clusters instead of squished against the axis. FlowJo's display transformation displays your data on an altered scale In the lower regions (first decade) and compress the view of data in the upper regions (fourth decade). This is because log scales expand the view of data The measurement error is the same in uncompensated samples, the variation becomes obvious when a compensated population has a low mean and therefore appears in the low regions of the log scale. The spreading of a population into negative compensated data values is the result of statistical error in measurement that is inherent in the data collected on flow cytometers. It is not possible to display "zero" or negative values. The cells become piled up in the first channel (against the axis) because the fluorescence parameters are displayed on a log scale where ![]() When data is properly compensated, it is common that a large number of cells are displayed squished against the axis. FlowJo offers a useful technique called Transformation for visualizing compensated data without producing artifactual peaks or having cells squished against the axes.
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