A.

of question may dictate parameters m

easur
Scope ed

Scope of question Intent in analysis Parameters measured

Abundance
Focused Targeted analysis
Expression
Broad Open-ended analysis Cellular Identity
Population Structure

High hts
-dim nsig
ensio
nal an i cipated i
alysis of unant
multiple parameters can identify

Examples:

Focused Cellular Identity Are distinct CD8 T cell phenotypes found during virus infection?

Broad Population Structure Does the distribution of cell populations differ between conditions?

B. CyTOF Algorithms

Cells viewed on a continuum Cells stratified into subpopulations

Unoptimized stratification Stratification with

statistical information
Optimized stratification

viSNE SPADE PhenoGraph X-shift Citrus

Number of model features

20 0 2 3 4 4 4 6 7 8 9 16 21 25 28 30
82258 82253
100

82261
82241
Model Cross Validation Error Rate

82251
75

82223

0 82228

82255
82265 82263

82229
82247
82262
82267
50

82259
82268 82236 82232

82264
82266 82256

-20
tSNE2

82249 82252
25

Model:
82250
82260

Min
82230 82243
82257

82254

SE
-30 0 30
0

82239
82234

Constrained
tSNE1 4.68 4.16 3.64 3.12 2.60 2.08 1.56 1.04 0.52 0.00

Regularization Threshold

Utility:
Rapid visual analysis, In depth visual analysis, Rapid statistical analysis,
limited quantitative analysis rapid quantitative analysis limited visual analysis

Data Output:
Abundance

Expression
Cellular Identity

Population Structure
Computational skills:
Beginner Advanced Intermediate

Figure 1
Kimball et al