Analysis Results

This section describes the results that are displayed by ModFit LT after an analysis has been performed. The results are usually displayed on the upper right side of the report, although you can move the results to anywhere on the report.

There are several types of models available in the program, each with its own set of results. Standard models are created by Automatic Analysis and by choosing a model for manual analysis. These models include components and results for debris, standards, aggregates, and apoptosis, as well as for one or more cycling populations. For each of the cell cycles, a G0G1, G2M, and S-Phase component is included.

Sync Wizard models are created when using the Sync Wizard. These models are designed for the special demands of perturbed cell cycle analysis.

The Cell Tracking Wizard creates Cell Tracking Wizard models. These models are used to study cell proliferation in samples using cell-tracking dyes and proliferation markers.

The program calculates percentages based on the number of events that are actually modeled. The number of events modeled can be less than the total number of events in a sample if you apply a gate, scale the data to eliminate events, or if the model itself does not fit the data exactly. Suppose, for example, that a listmode file contains 10,000 events. If you gate out 10% of the events, the analysis will be performed on 9,000 events, or 90% of the total events.

Standard Models

Label	Description
Model	This shows the name of the model used for the analysis. For information on how to decode model names, see Model Descriptions.
Analysis type:	This will show either "Automatic analysis" or "Manual analysis", depending on how the model was selected and whether any user-edits were made to the model set up.
Auto Linearity	This will show "Yes" if Auto Linearity was performed, or "No" if it was not.
Ploidy Mode	Displays the Auto Analysis Diploid Determination setting.
Diploid Reference	If the Diploid Determination setting is External Reference, Based on Standard 1, or Based on Standard 2, this result will display the location of the ploidy reference. If First Cycle is Diploid mode, this result is meaningless and is not displayed.
% Cycle	Percent of all events that are associated with cycling populations
%G0G1	G0G1 as a percent of all cells in that cycle
G0G1 mean	G0G1 mean channel
%G2M	G2M as a percent of all cells in that cycle
G2M mean	G2M mean channel
% S-Phase	S-Phase as a percent of all cells in that cycle
G2/G1 ratio	Ratio of G2 mean channel to G1 mean channel
%CV	Coefficient of variation for G0G1 cells
DI	DNA Index, defined as the mean channel of G1 cells of an aneuploid population compared to Diploid G1 mean channel.
DI based on reference	If the Diploid Determination setting is External Reference, Based on Standard 1, or Based on Standard 2, this result will display the DNA index based on the computed reference position for the Diploid G1.

Total Aneuploid S-Phase	Sum of all Aneuploid S-Phase areas as a percentage of the total (G1G1 + S + G2M) area for all Aneuploid populations. This result is not displayed for Diploid models. However it is computed as a keyword even for Diploid models. For Diploid models, the "tumor" S-Phase is considered to be the Diploid S-Phase, and so the keyword reports the S-Phase of the Diploid.
Total S-Phase	Also called "Average S-Phase". Sum of all S-Phase areas as a percentage of the total area for cycling cells of all populations.
Total B.A.D	Amount of debris and aggregates found within the region between the first G1 and the last G2 peak.

Standards
Stnd %	Area of standard as a % of all modeled events minus debris
Stnd mean	Mean channel position of standard
DI	DNA Index of standard as standard mean channel relative to the Diploid G1 mean channel.
Dip G1 Ratio	Diploid G1 mean channel divided by mean channel of the standard
%CV	Coefficient of variation for standard

%Debris	Debris area as a % of all modeled events
%Aggregates	Aggregate area as a % of all modeled events
%Apoptosis	Apoptosis area as a percent of all modeled events minus debris
Modeled events	Number of events accounted for by all components in the model
All cycle events	Number of modeled events in the G0G1, G2M, and S-Phase components of all cycling populations
Cycle events per channel	All cycle events divided by the number of channels between the first G0G1 and the last G2M of the model.
nRCS	Normalized reduced chi-square, a measure of goodness of fit. This produces an RCS equivalent results as if the sample file contained 10,000 events. See Options and Configuration for more information on this statistic.
RCS	Reduced chi-square, a measure of goodness of fit. Values from 1.0 to 3.0 are good, 3.0 to 5.0 are fair, and greater than 5.0 are poor. Note, RCS will increase as the number of events in the sample file increase. The nRCS can be used in cases where samples routinely have 50,000 or more events.

Tetraploid Model

ModFit LT handles Tetraploid histograms slightly differently than most other ploidy types. Because the Diploid G2M and the Tetraploid G1 peaks are superimposed, the program disables the Diploid G2M during the modeling process. After the model has been applied to the histogram using the Fit with Current Model command or Auto Analysis, the program will add back a specified amount to the Diploid G2M and reduce the Tetraploid G1 by the same amount. This amount is computed as a percentage of the Diploid G1 peak, and the percentage is specified in the Options and Configuration dialog box. The default percentage is 8% (0.08).

Sync Wizard Model

In addition to many of the results described for standard models, the Sync Wizard also computes the percentage for sub-compartments of S-Phase

Result	Computation
S-Phase	Cells in S-Phase as a percent of all the cells in that cycling population
Compartment n	Area of S-Phase sub compartment as a percent of all the cells in that cycling population

Cell Tracking Wizard Model

See the Cell Tracking Example for an explanation of Cell Tracking results.