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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.

From: Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering

(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