Input Elements  Output Elements  
PlateView  Manipulate samples 
Heatmap  Overview of all samples and probes 
Experiment
Table 
Manipulate experiments 
Bargraph 
Show probes and/or samples 
Sample
Table 
Manipulate samples 
Differential Expression
Table 
Show pvalue ranked differential expression 
Probe
Table 
Manipulate probes 
Variable Data Chart 
Show selected probes broken out by group 
Variable Table 
Manipulate variables 
Volcano
Plot 
Show pvalue / fold expression chart 
Pair
Plot 
Compare a pair of probes or samples

Stability
Plot 
Probe suitability for normalization

Buttons  Other
actions 

Load
Button 
Bring data from disk into memory

Menus 
The top menu bar 
Experiment Button 
Create experiments 
FDE 
Quick access to the FirePlex Discovery Engine 
Negative Button 
Mark negative samples 
Selection  Selecting probes, samples, experiments 
Normalize Button 
Toggle normalization status 
Zoom & pan  Moving around charts 
Export
Button 
Save data from memory back to disk 
Tables 
General info about tables 
Clear
Button 
Empty memory 
Variable Definition 
How to define variables 
Files  Concepts 

FCS file  Flow cytometry data  Work flow  Samples vs plates vs experiments 
FWS file  FirePlex workspace  Experiment  Group of samples for statistical processing 
PLX
file 
Barcoded probe definition 
Plate  Group of samples for visual selection 
Sample
Sheet 
Plate layout definition 
Variable  Basis for differential analysis 
Standard Curve 
Quantification using known standards 
MDD  Minimum detectable dose 
Sample quality  Data quality in a particular sample 
Data
Processing 
Calculating target levels in each sample from flow cytometry events 
Data Statistics 
How the mean, standard deviation and confidence intervals are calculated 
Normalization 
Motivation, algorithms and experience with normalization 
Clustering 
Hierarchical clustering used to organize the heatmap 
Differential Analysis 
Using variables to analyze differential expression between groups of samples 
Multiple Comparisons 
Calculating pvalues in a multiplex context 
Anova with repeated measures 
Differential analysis of a primary variable, controlling for secondary variables. 