Table 2 Cluster accuracy and stability on the completely synthetic data with four repeated measurements at low noise level
From: Clustering gene-expression data with repeated measurements
(a) Cluster accuracy* | ||||||
|---|---|---|---|---|---|---|
Algorithm | Similarity measure/model | Average | SD-weighted | CV-weighted | FITSS | IMM |
Average linkage | Elliptical | NA | NA | NA | NA | 0.957 (0.089) |
Complete linkage | Elliptical | NA | NA | NA | NA | 0.957 (0.090) |
MCLUST-HC | NA | 0.930 (0.100) | NA | NA | 0.902 (0.123) | NA |
Average linkage | Distance | 0.877 (0.191) | 0.927 (0.100) | 0.876 (0.192) | 0.804 (0.155) | NA |
Centroid linkage | Distance | 0.840 (0.178) | 0.927 (0.100) | 0.927 (0.100) | 0.840 (0.178) | NA |
k-means | Distance | 0.877 (0.191) | 0.927 (0.100) | 0.876 (0.192) | NA | NA |
Average linkage | Spherical | NA | NA | NA | NA | 0.926 (0.102) |
Complete linkage | Distance | 0.925 (0.102) | 0.876 (0.192) | 0.925 (0.103) | 0.840 (0.179) | NA |
Complete linkage | Spherical | NA | NA | NA | NA | 0.897 (0.088) |
Centroid linkage | Correlation | 0.765 (0.115) | 0.575 (0.179) | 0.527 (0.141) | 0.765 (0.115) | NA |
Average linkage | Correlation | 0.764 (0.114) | 0.576 (0.201) | 0.597 (0.210) | 0.718 (0.222) | NA |
k-means | Correlation | 0.764 (0.114) | 0.707 (0.140) | 0.652 (0.116) | NA | NA |
Complete linkage | Correlation | 0.755 (0.116) | 0.584 (0.189) | 0.599 (0.194) | 0.609 (0.201) | NA |
(b) Cluster stability†| ||||||
Algorithm | Similarity measure/model | Average | SD-weighted | CV-weighted | FITSS | IMM |
Average linkage | Distance | 0.970 (0.055) | 0.998 (0.003) | 0.998 (0.002) | 0.979 (0.018) | NA |
Centroid linkage | Distance | 0.984 (0.025) | 0.998 (0.002) | 0.986 (0.027) | 0.984 (0.025) | NA |
k-means | Distance | 0.954 (0.062) | 0.998 (0.003) | 0.967 (0.070) | NA | NA |
Average linkage | Correlation | 0.958 (0.054) | 0.832 (0.095) | 0.854 (0.060) | 0.984 (0.025) | NA |
Complete linkage | Distance | 0.968 (0.041) | 0.923 (0.131) | 0.981 (0.037) | 0.918 (0.055) | NA |
Average linkage | Elliptical | NA | NA | NA | NA | 0.961 (0.081) |
Complete linkage | Elliptical | NA | NA | NA | NA | 0.960 (0.083) |
Centroid linkage | Correlation | 0.959 (0.054) | 0.861 (0.119) | 0.866 (0.026) | 0.959 (0.054) | NA |
k-means | Correlation | 0.958 (0.054) | 0.693 (0.144) | 0.634 (0.098) | NA | NA |
Complete linkage | Correlation | 0.947 (0.067) | 0.580 (0.140) | 0.671 (0.100) | 0.915 (0.049) | NA |
MCLUST-HC | NA | 0.935 (0.089) | NA | NA | 0.916 (0.066) | NA |
Average linkage | Spherical | NA | NA | NA | NA | 0.852 (0.089) |
Complete linkage | Spherical | NA | NA | NA | NA | 0.779 (0.091) |