Units

The output of a statistical calculation can be displayed in units of either fluorescence intensity (also known as RFI) or in channel numbers. The RFI takes into account scaling factors such as whether or not logarithmic amplification is used, or, if linear amplification is used, it takes into account the gain setting on the parameter (e.g., 1x, 2x, etc.). Expressing the statistics in units of channels ignores all scaling information provided by the FCS header, and uses a linear scale of 0 to the maximum value defined by the data collection program (generally, 255, 1023, or 4095). In general, you should use the statistics that give you RFI units except for specialized applications.

Note that if you use the Calibration Platform to calibrate a fluorescence parameter to absolute units, then all statistics computed on the calibrated platform are given in terms of those units (for example, absolute number of molecules per cell).

Definition of statistics

Median - The median is the fluorescence value below which 50% of the events are found; i.e., it is the 50th percentile in fluorescence. In general, the median is a better estimator of the central tendency of a population than the mean, especially for log-amplified data.

Mean - The arithmetic mean of the data. This means the linear scaled fluorescence are averaged; the result is weighted by outliers at the high end of the distribution.

Mode - The fluorescence value which is most frequently found for a given parameter. This is the same position at which the highest point on a histogram plot is found.

Geom. Mean - The geometric mean of the data. The log of the fluorescence is averaged; the scale value of this average is reported (i.e., in fluorescence units).

Robust CV - The spread which encloses the central 63% of the event; roughly equivalent to one standard deviation. This metric is not affect by outlying events, and is identical to the CV for normal distributions.

CV - The coefficient of variation of the entire data set.

%ile - Percentile. This is the fluorescence below which n% of the events are found, where n is the selected value. n=50 is equivalent to the median.

Frequency - The percentage of cells in this gate out of the total sample.

Freq. of Parent - The percentage of cells in this gate out of the parent gate (one level up).

Freq. of Grandparent - The percentage of cells in this gate out of the gate two levels up.

Count - The absolute number of cells in this gate.