Statistics

Drawing events in a plot is nice, but having numbers to back the results up is even better. FCSalyzer allows the usual type of statistics to be calculated for the plots.

You can generate statistics for the selected plots by using the "Statistics" command from the "Plot" menu bar item. In the statistics dialog, you can select the statistics you want to have calculated. The statistics for regions, gates, markers and quadrants are all selected here and can be computed in parallel. For each region etc, the usual statistical values can be calculated: number of events, percentages, peak channel, mean and median fluorescence intensities. Please note: the regular mean, not the geometric mean, is calculated for the data.

To change already existing statistics, select the statistics to change, then use the "Edit statistics" command from the "Plot" menu bar item. These settings will be the default for all successively generated statistics.

A word of advice: as far as I can say, the calculated statistics are exactly the same values as are calculated by BD CellQuest(tm). However, you should definitely cross-check the analysis with your regular analysis program to make sure that FCSalyzer didn't make a mistake in the calculations.

Technical note: FCSalyzer creates temporary files for calculating statistics. These files are generated using standard Java procedures and the details for that rest with the Java Environment installed on the user's computer system. The temporary files should thus be generated inside the standard file location for temporary files (such as "temp") and should be deleted automatically when FCSalyzer closes. These files only contain numbers used for calculation, and no further data. If the statistics calculations fail, make sure that FCSalyzer is able to generate temporary files on your computer system.

BD CellQuest is a trademark of BD Biosciences