Table 2 Influence of the replacement method on the Conserved Pairs Proportion (CPP). The numbers of clusters defined per metric are indicated (Kalgo). The CPP and CPP f values are given for the (1/7) subset of Ogawa [26] with missing values introduced (a) in the entire subsets and (b) only in extreme values (values > 1.5 or < -1.5). The CPP was computed by using the seven algorithms on the data without replacing the MVs (MV), after replacing the MVs by the kNN method (kNN) with the k opt values (see Table 3), or, after replacing the MVs by zero (zero). For kNN and zero values, the CPP and CPP f (with f = 5) values are given in (%). The percent of gain for all the simulations is indicated (+/-), i.e. the proportion of simulations with a better CPP value than the CPP value of MV. The values given in this table are the average values for MV in the range [1%; 50%] of genes with one MV per genes.
(a) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
CPP | CPP f | ||||||||||
MV | kNN | zero | MV | kNN | zero | ||||||
Algorithm | K algo | (%) | (%) | (+/-) | (%) | (+/-) | (%) | (%) | (+/-) | (%) | (+/-) |
single | 175 | 96.4 | 98.3 | 99.3 | 98.2 | 99.6 | 98.8 | 99.1 | 53.7 | 99.0 | 47.8 |
centroid | 175 | 95.3 | 96.0 | 74.8 | 95.7 | 64.1 | 97.7 | 97.9 | 57.6 | 97.8 | 53.3 |
average | 83 | 73.2 | 75.3 | 66.3 | 74.8 | 62.0 | 92.0 | 92.5 | 54.4 | 93.0 | 57.6 |
median | 165 | 70.1 | 71.5 | 55.2 | 72.2 | 54.4 | 85.2 | 86.0 | 52.8 | 86.2 | 52.1 |
mcquitty | 48 | 58.2 | 59.1 | 54.5 | 58.6 | 50.1 | 74.9 | 75.3 | 51.9 | 75.1 | 49.5 |
Ward | 19 | 51.0 | 52.4 | 62.4 | 50.7 | 49.1 | 71.8 | 73.3 | 60.2 | 71.5 | 49.1 |
complete | 36 | 47.9 | 49.2 | 60.4 | 48.4 | 51.9 | 71.9 | 72.7 | 53.7 | 72.1 | 51.6 |
(b) | |||||||||||
CPP | CPP f | ||||||||||
MV | kNN | zero | MV | kNN | zero | ||||||
Algorithm | K algo | (%) | (%) | (+/-) | (%) | (+/-) | (%) | (%) | (+/-) | (%) | (+/-) |
single | 175 | 97.9 | 98.4 | 98.5 | 98.7 | 98.3 | 98.8 | 99.3 | 86.9 | 99.7 | 76.6 |
centroid | 175 | 96.5 | 96.7 | 64.8 | 96.8 | 60.6 | 98.5 | 98.5 | 55.9 | 97.7 | 32.8 |
average | 83 | 81.4 | 81.0 | 45.1 | 83.3 | 66.1 | 93.9 | 94.5 | 57.0 | 94.9 | 61.3 |
median | 165 | 75.0 | 74.2 | 45.7 | 74.2 | 47.9 | 87.0 | 86.5 | 50.3 | 85.1 | 45.4 |
mcquitty | 48 | 71.6 | 71.3 | 48.1 | 71.9 | 51.0 | 83.1 | 83.2 | 49.6 | 84.6 | 58.2 |
Ward | 19 | 63.8 | 62.4 | 42.1 | 60.8 | 29.9 | 83.0 | 81.1 | 37.1 | 79.8 | 27.0 |
complete | 36 | 56.5 | 55.2 | 44.5 | 56.0 | 47.2 | 75.7 | 74.6 | 46.1 | 74.6 | 45.0 |