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Table 4 Summary of internal evaluations for each compared methods

From: A comparison framework and guideline of clustering methods for mass cytometry data

Datasets

Methods

Internal evaluations

CH

DB

XB

Cell Cycle

Accense

3.2409 ± 0.2069

2.4746 ± 0.2563

0.6473 ± 0.0750

PhenoGraph

3.4250 ± 0.0350

2.5692 ± 0.1503

0.7864 ± 0.0392

Xshift

3.5620 ± 0.0443

1.7337 ± 0.1618

0.9131 ± 0.3066

kmeans

3.9414 ± 0.0011

1.5971 ± 0.0013

0.7705 ± 0.0165

flowMeans

3.5992 ± 0.0283

1.6237 ± 0.0341

0.7294 ± 0.0393

FlowSOM

3.6294 ± 0.0036

1.3578 ± 0.0351

0.6669 ± 0.0269

DEPECHE

3.8372 ± 0.0283

1.7767 ± 0.0322

0.7695 ± 0.0177

ACDC

3.4645 ± 0.0901

2.0773 ± 0.3156

0.9395 ± 0.0428

LDA

3.4581 ± 0.0036

2.5080 ± 0.0191

1.0021 ± 0.0358

Colon

Accense

3.2688 ± 0.0622

1.7064 ± 0.0656

1.0427 ± 0.0545

PhenoGraph

3.4231 ± 0.0194

1.9030 ± 0.0245

1.3997 ± 0.1199

Xshift

3.0706 ± 0.0179

2.3218 ± 0.0595

1.3207 ± 0.0511

kmeans

3.5109 ± 0.0079

1.9037 ± 0.0501

1.4570 ± 0.1055

flowMeans

3.4793 ± 0.1068

1.5864 ± 0.0421

1.6706 ± 0.1958

FlowSOM

3.6435 ± 0.0117

1.6583 ± 0.0514

1.5910 ± 0.1568

DEPECHE

3.9819 ± 0.0375

1.7725 ± 0.0250

1.6325 ± 0.0930

ACDC

3.5898 ± 0.0440

2.0607 ± 0.1160

1.4239 ± 0.0754

LDA

3.5100 ± 0.0009

2.1773 ± 0.0065

1.5564 ± 0.0724

Levine13dim

Accense

3.4230 ± 0.0932

1.8832 ± 0.1408

1.2321 ± 0.0278

PhenoGraph

4.0739 ± 0.0176

1.4645 ± 0.0346

1.3972 ± 0.1349

Xshift

3.5106 ± 0.0289

2.4284 ± 0.0443

1.7868 ± 0.0476

kmeans

3.8508 ± 0.0150

2.1550 ± 0.0546

1.6213 ± 0.1471

flowMeans

4.0475 ± 0.0194

1.5030 ± 0.0849

1.4234 ± 0.1182

FlowSOM

3.8486 ± 0.0071

1.7564 ± 0.0615

1.5043 ± 0.1531

DEPECHE

4.2783 ± 0.0174

1.1677 ± 0.0342

1.3562 ± 0.0392

ACDC

3.9638 ± 0.0110

1.4916 ± 0.0370

1.3109 ± 0.0948

LDA

3.8288 ± 0.0106

2.0046 ± 0.0493

1.3828 ± 0.1167

Levine32dim

Accense

3.4621 ± 0.0901

2.3414 ± 0.0925

0.7891 ± 0.0950

PhenoGraph

3.7401 ± 0.0081

1.8293 ± 0.0810

1.0009 ± 0.0479

Xshift

3.6669 ± 0.0102

2.2576 ± 0.1324

0.8295 ± 0.1382

kmeans

3.8761 ± 0.0166

2.0587 ± 0.0386

0.9972 ± 0.0441

flowMeans

3.8546 ± 0.0393

1.6975 ± 0.2199

0.7985 ± 0.0709

FlowSOM

3.8244 ± 0.0285

1.5974 ± 0.0863

0.8366 ± 0.0792

DEPECHE

4.1480 ± 0.0009

1.4727 ± 0.0023

0.7575 ± 0.0351

ACDC

3.6169 ± 0.0046

1.3974 ± 0.0049

0.7693 ± 0.1310

LDA

3.8297 ± 0.0007

1.7011 ± 0.0099

0.7155 ± 0.0139

Muscle

Accense

3.2254 ± 0.1688

2.3190 ± 0.3178

0.8420 ± 0.1211

PhenoGraph

3.6052 ± 0.0132

1.8619 ± 0.0417

1.7228 ± 0.2389

Xshift

3.2898 ± 0.0274

2.2460 ± 0.1524

2.1455 ± 0.1599

kmeans

3.9722 ± 0.0022

1.7729 ± 0.0099

1.4987 ± 0.1212

flowMeans

3.3809 ± 0.0565

1.7685 ± 0.0769

1.3750 ± 0.1428

FlowSOM

3.8262 ± 0.0146

1.4439 ± 0.0462

1.3586 ± 0.1473

DEPECHE

4.2639 ± 0.0044

1.2235 ± 0.0080

1.2892 ± 0.0269

ACDC

3.6900 ± 0.0305

1.7186 ± 0.0515

1.5641 ± 0.15555

LDA

3.8073 ± 0.0031

1.6641 ± 0.0206

1.6003 ± 0.0900

Samusik01

Accense

3.2952 ± 0.0476

2.3424 ± 0.1454

0.6500 ± 0.0266

PhenoGraph

3.7380 ± 0.0033

1.4607 ± 0.0424

0.7669 ± 0.0831

Xshift

3.2660 ± 0.0134

2.7855 ± 0.4644

1.2670 ± 0.1654

kmeans

3.7087 ± 0.0135

2.2072 ± 0.0854

0.9365 ± 0.0792

flowMeans

3.4029 ± 0.0381

1.6069 ± 0.2374

0.6309 ± 0.0475

FlowSOM

3.6941 ± 0.0257

1.8967 ± 0.3799

0.8286 ± 0.0832

DEPECHE

4.1028 ± 0.0021

1.4867 ± 0.0054

0.9141 ± 0.0109

ACDC

3.6827 ± 0.0178

1.3871 ± 0.0132

0.7273 ± 0.0573

LDA

3.6767 ± 0.0080

1.6325 ± 0.0242

1.0414 ± 0.0808

  1. Data shown as mean ± standard deviation. CH Calinski-Harabasz index (log10 transformed), DB Davies-Bouldin index, XB Xie-Beni index (log10 transformed)