From: Integrating heterogeneous genomic data to accurately identify disease subtypes
Scale issue | Data1 | Data2 | Concatenation | SNF | iBFE1 | iBFE2 | iBFE2 |
---|---|---|---|---|---|---|---|
PCCintraclass | 0.023 ± 0.0011 | 0.025 ± 0.0019 | 0.031 ± 0.0034 | 0.17 ± 0.0067 | 0.30 ± 0.012 | 0.23 ± 0.014 | 0.28 ± 0.015 |
PCCinterclass | −0.0018 ± 0.00021 | −0.0067 ± 0.00033 | 0.0068 ± 0.00035 | 0.15 ± 0.0054 | −0.30 ± 0.013 | −0.21 ± 0.015 | −0.26 ± 0.015 |
PCCintraclass-PCCinterclass | 0.024 ± 0.0014 | 0.031 ± 0.0020 | 0.024 ± 0.0035 | 0.021 ± 0.012 | 0.60 ± 0.022 | 0.44 ± 0.024 | 0.54 ± 0.025 |
Simintraclass | 0.02 ± 0.0023 | 0.02 ± 0.0022 | 0.02 ± 0.0023 | 0.97 ± 0.004 | 0.32 ± 0.011 | 0.23 ± 0.012 | 0.29 ± 0.010 |
Siminterclass | 0 ± 0.0 | 0 ± 0.0 | 0 ± 0.0 | 0.97 ± 0.005 | 0.22 ± 0.012 | 0.17 ± 0.013 | 0.22 ± 0.013 |
Simintraclass-Siminterclass | 0.02 ± 0.0023 | 0.02 ± 0.0022 | 0.02 ± 0.0023 | 0.00057 ± 0.0011 | 0.10 ± 0.022 | 0.06 ± 0.025 | 0.07 ± 0.023 |
ACC_rfLOO | 0.59 ± 0.057 | 0.95 ± 0.032 | 0.94 ± 0.045 | 0.52 ± 0.062 | 0.99 ± 0.035 | 0.99 ± 0.036 | 0.99 ± 0.036 |
NMI_kmeans | 0.035 ± 0.0085 | 0.035 ± 0.0089 | 0.035 ± 0.0093 | 0.0052 ± 0.0012 | 0.93 ± 0.054 | 0.92 ± 0.051 | 0.93 ± 0.055 |
Noise type | |||||||
PCCintraclass | 0.025 ± 0.0031 | 0.066 ± 0.0022 | 0.13 ± 0.014 | 0.013 ± 0.0029 | 0.32 ± 0.034 | 0.23 ± 0.030 | 0.31 ± 0.031 |
PCCinterclass | −0.0040 ± 0.00097 | −0.049 ± 0.0012 | 0.097 ± 0.0023 | −0.011 ± 0.0058 | −0.32 ± 0.031 | −0.22 ± 0.029 | −0.29 ± 0.033 |
PCCintraclass-PCCinterclass | 0.029 ± 0.0032 | 0.12 ± 0.0024 | 0.033 ± 0.016 | 0.024 ± 0.0067 | 0.64 ± 0.061 | 0.45 ± 0.059 | 0.60 ± 0.063 |
Simintraclass | 0.02 ± 0.0023 | 0.02 ± 0.0025 | 0.02 ± 0.0026 | 0.99 ± 0.0007 | 0.27 ± 0.012 | 0.25 ± 0.015 | 0.28 ± 0.013 |
Siminterclass | 0 ± 0.0 | 0 ± 0.0 | 0 ± 0.0 | 0.99 ± 0.0014 | 0.16 ± 0.009 | 0.15 ± 0.011 | 0.16 ± 0.011 |
Simintraclass-Siminterclass | 0.02 ± 0.0023 | 0.02 ± 0.0025 | 0.02 ± 0.0026 | 0.00021 ± 0.0020 | 0.11 ± 0.020 | 0.10 ± 0.026 | 0.12 ± 0.023 |
ACC_rfLOO | 0.54 ± 0.023 | 0.98 ± 0.015 | 0.97 ± 0.021 | 0.93 ± 0.013 | 0.96 ± 0.015 | 0.95 ± 0.016 | 0.96 ± 0.018 |
NMI_kmeans | 0.015 ± 0.0021 | 0.82 ± 0.0023 | 0.024 ± 0.0033 | 0.0042 ± 0.00056 | 0.83 ± 0.017 | 0.82 ± 0.018 | 0.82 ± 0.015 |
Noise size | |||||||
PCCintraclass | 0.023 ± 0.0031 | 0.048 ± 0.0015 | 0.026 ± 0.0033 | 0.0070 ± 0.00067 | 0.13 ± 0.038 | 0.09 ± 0.023 | 0.11 ± 0.031 |
PCCinterclass | −0.0041 ± 0.00009 | −0.028 ± 0.0012 | −0.0071 ± 0.00013 | −0.0045 ± 0.00021 | −0.13 ± 0.037 | −0.08 ± 0.025 | −0.10 ± 0.033 |
PCCintraclass-PCCinterclass | 0.027 ± 0.0031 | 0.076 ± 0.0024 | 0.033 ± 0.0034 | 0.012 ± 0.00069 | 0.26 ± 0.065 | 0.17 ± 0.049 | 0.21 ± 0.061 |
Simintraclass | 0.02 ± 0.0014 | 0.02 ± 0.0011 | 0.02 ± 0.0015 | 0.99 ± 0.00002 | 0.26 ± 0.015 | 0.19 ± 0.016 | 0.23 ± 0.017 |
Siminterclass | 0 ± 0.0 | 0 ± 0.0 | 0 ± 0.0 | 0.99 ± 0.00003 | 0.20 ± 0.017 | 0.16 ± 0.016 | 0.18 ± 0.018 |
Simintraclass-Siminterclass | 0.02 ± 0.0014 | 0.02 ± 0.0011 | 0.02 ± 0.0015 | 0.00016 ± 0.0006 | 0.06 ± 0.027 | 0.03 ± 0.030 | 0.05 ± 0.033 |
ACC_rfLOO | 0.59 ± 0.051 | 0.84 ± 0.034 | 0.82 ± 0.054 | 0.86 ± 0.041 | 0.91 ± 0.052 | 0.90 ± 0.053 | 0.91 ± 0.055 |
NMI_kmeans | 0.024 ± 0.0081 | 0.58 ± 0.043 | 0.028 ± 0.0097 | 0.0019 ± 0.00091 | 0.56 ± 0.062 | 0.55 ± 0.055 | 0.57 ± 0.063 |
Partial clustering | |||||||
PCCintraclass | 0.049 ± 0.0038 | 0.046 ± 0.0042 | 0.06 ± 0.0021 | 0.027 ± 0.0023 | 0.13 ± 0.05 | 0.10 ± 0.04 | 0.12 ± 0.06 |
PCCinterclass | 0.0010 ± 0.00085 | −0.0011 ± 0.00092 | −0.016 ± 0.0034 | −0.025 ± 0.0026 | −0.11 ± 0.023 | −0.10 ± 0.024 | −0.12 ± 0.025 |
PCCintraclass-PCCinterclass | 0.048 ± 0.0043 | 0.048 ± 0.0047 | 0.079 ± 0.0070 | 0.053 ± 0.0049 | 0.24 ± 0.067 | 0.20 ± 0.062 | 0.24 ± 0.073 |
Simintraclass | 0.02 ± 0.0041 | 0.02 ± 0.0044 | 0.02 ± 0.0063 | 0.99 ± 0.00011 | 0.27 ± 0.019 | 0.23 ± 0.020 | 0.25 ± 0.022 |
Siminterclass | 0 ± 0.0 | 0 ± 0.0 | 0 ± 0.0 | 0.99 ± 0.00012 | 0.21 ± 0.021 | 0.18 ± 0.021 | 0.20 ± 0.021 |
Simintraclass-Siminterclass | 0.02 ± 0.0041 | 0.02 ± 0.0044 | 0.02 ± 0.0063 | 0.00040 ± 0.00022 | 0.061 ± 0.033 | 0.052 ± 0.035 | 0.057 ± 0.038 |
ACC_rfLOO | 0.86 ± 0.028 | 0.87 ± 0.026 | 0.93 ± 0.016 | 0.96 ± 0.029 | 0.90 ± 0.023 | 0.89 ± 0.031 | 0.91 ± 0.035 |
NMI_kmeans | 0.65 ± 0.033 | 0.61 ± 0.032 | 0.90 ± 0.028 | 0.63 ± 0.035 | 0.57 ± 0.031 | 0.55 ± 0.035 | 0.59 ± 0.039 |
Conflicting clustering | |||||||
PCCintraclass | 0.095 ± 0.0052 | 0.095 ± 0.0051 | 0.095 ± 0.0061 | 0.032 ± 0.0063 | 0.62 ± 0.023 | 0.53 ± 0.033 | 0.59 ± 0.035 |
PCCinterclass | −0.017 ± 0.0047 | −0.020 ± 0.0049 | −0.019 ± 0.0062 | −0.0099 ± 0.0067 | −0.20 ± 0.019 | −0.18 ± 0.021 | −0.19 ± 0.022 |
PCCintraclass-PCCinterclass | 0.11 ± 0.011 | 0.12 ± 0.012 | 0.11 ± 0.013 | 0.042 ± 0.015 | 0.82 ± 0.037 | 0.71 ± 0.045 | 0.78 ± 0.051 |
Simintraclass | 0.038 ± 0.0061 | 0.038 ± 0.0062 | 0.038 ± 0.0061 | 0.99 ± 0.00005 | 0.31 ± 0.024 | 0.27 ± 0.025 | 0.30 ± 0.029 |
Siminterclass | 0 ± 0.0 | 0 ± 0.0 | 0 ± 0.0 | 0.99 ± 0.00007 | 0.11 ± 0.021 | 0.10 ± 0.020 | 0.12 ± 0.023 |
Simintraclass-Siminterclass | 0.038 ± 0.0061 | 0.038 ± 0.0062 | 0.038 ± 0.0061 | 0.00019 ± 0.00010 | 0.20 ± 0.037 | 0.17 ± 0.039 | 0.18 ± 0.042 |
ACC_rfLOO | 0.42 ± 0.020 | 0.51 ± 0.023 | 0.63 ± 0.031 | 0.93 ± 0.063 | 0.96 ± 0.034 | 0.94 ± 0.031 | 0.95 ± 0.036 |
NMI_kmeans | 0.46 ± 0.033 | 0.49371 ± 0.034 | 0.84626 ± 0.045 | 0.11654 ± 0.081 | 0.92 ± 0.052 | 0.91 ± 0.053 | 0.92 ± 0.055 |