Table 3 |
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|
Estimating the number of clusters in simulated data |
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|
Method |
Number of clusters, |
|||||
|
|
||||||
|
Model 1 |
||||||
|
1* |
2 |
3 |
4 |
5 |
>5 |
|
|
Clest |
48 |
2 |
0 |
0 |
0 |
0 |
|
gap |
48 |
0 |
1 |
1 |
0 |
0 |
|
gapPC |
50 |
0 |
0 |
0 |
0 |
0 |
|
sil |
- |
37 |
6 |
4 |
3 |
0 |
|
ch |
- |
42 |
7 |
1 |
0 |
0 |
|
kl |
- |
12 |
14 |
11 |
13 |
0 |
|
hart |
0 |
5 |
22 |
16 |
7 |
0 |
|
Model 2 |
||||||
|
1 |
2 |
3* |
4 |
5 |
>5 |
|
|
Clest |
0 |
1 |
49 |
0 |
0 |
0 |
|
gap |
0 |
0 |
50 |
0 |
0 |
0 |
|
gapPC |
0 |
0 |
50 |
0 |
0 |
0 |
|
sil |
- |
5 |
45 |
0 |
0 |
0 |
|
ch |
- |
0 |
50 |
0 |
0 |
0 |
|
kl |
- |
0 |
41 |
2 |
7 |
0 |
|
hart |
0 |
0 |
0 |
2 |
2 |
46 |
|
Model 3 |
||||||
|
1 |
2 |
3 |
4* |
5 |
>5 |
|
|
Clest |
0 |
1 |
20 |
29 |
0 |
0 |
|
gap |
0 |
1 |
16 |
33 |
0 |
0 |
|
gapPC |
0 |
1 |
12 |
37 |
0 |
0 |
|
sil |
- |
17 |
24 |
9 |
0 |
0 |
|
ch |
- |
8 |
20 |
22 |
0 |
0 |
|
kl |
- |
3 |
11 |
35 |
1 |
0 |
|
hart |
0 |
0 |
8 |
42 |
0 |
0 |
|
Model 4 |
||||||
|
1 |
2 |
3 |
4* |
5 |
>5 |
|
|
Clest |
0 |
0 |
1 |
49 |
0 |
0 |
|
gap |
0 |
0 |
0 |
50 |
0 |
0 |
|
gapPC |
0 |
0 |
1 |
49 |
0 |
0 |
|
sil |
- |
5 |
8 |
37 |
0 |
0 |
|
ch |
- |
5 |
7 |
38 |
0 |
0 |
|
kl |
- |
0 |
1 |
49 |
0 |
0 |
|
hart |
0 |
0 |
0 |
50 |
0 |
0 |
|
Model 5 |
||||||
|
1 |
2* |
3 |
4 |
5 |
>5 |
|
|
Clest |
0 |
44 |
0 |
6 |
0 |
0 |
|
gap |
0 |
0 |
0 |
19 |
31 |
0 |
|
gapPC |
0 |
50 |
0 |
0 |
0 |
0 |
|
sil |
- |
50 |
0 |
0 |
0 |
0 |
|
ch |
- |
3 |
0 |
47 |
0 |
0 |
|
kl |
- |
50 |
0 |
0 |
0 |
0 |
|
hart |
0 |
0 |
0 |
0 |
0 |
50 |
|
Model 6 |
||||||
|
1 |
2* |
3 |
4 |
5 |
>5 |
|
|
Clest |
0 |
43 |
7 |
0 |
0 |
0 |
|
gap |
47 |
3 |
0 |
0 |
0 |
0 |
|
gapPC |
43 |
5 |
1 |
1 |
0 |
0 |
|
sil |
- |
41 |
5 |
4 |
0 |
0 |
|
ch |
- |
43 |
5 |
2 |
0 |
0 |
|
kl |
- |
16 |
9 |
17 |
8 |
0 |
|
hart |
0 |
1 |
0 |
5 |
14 |
30 |
|
Model 7 |
||||||
|
1 |
2* |
3 |
4 |
5 |
>5 |
|
|
Clest |
26 |
15 |
6 |
3 |
0 |
0 |
|
gap |
25 |
22 |
2 |
1 |
0 |
0 |
|
gapPC |
31 |
17 |
2 |
0 |
0 |
0 |
|
sil |
- |
42 |
6 |
1 |
1 |
0 |
|
ch |
- |
39 |
10 |
0 |
1 |
0 |
|
kl |
- |
13 |
15 |
10 |
12 |
0 |
|
hart |
6 |
39 |
5 |
0 |
0 |
0 |
|
Model 8 |
||||||
|
1 |
2* |
3 |
4 |
5 |
>5 |
|
|
Clest |
0 |
16 |
34 |
0 |
0 |
0 |
|
gap |
0 |
22 |
28 |
0 |
0 |
0 |
|
gapPC |
0 |
28 |
21 |
1 |
0 |
0 |
|
sil |
- |
50 |
0 |
0 |
0 |
0 |
|
ch |
- |
50 |
0 |
0 |
0 |
0 |
|
kl |
- |
25 |
17 |
4 |
4 |
0 |
|
hart |
0 |
3 |
43 |
4 |
0 |
0 |
|
|
||||||
|
For each simulation model, the distribution of the estimated number of clusters is
recorded for each method. The true number of clusters is denoted by the asterisk and
the modes for the distribution of the 50 estimates are indicated in bold for each
method. Note that sil, ch, and kl do not have the ability to estimate |
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|
Dudoit and Fridlyand Genome Biology 2002 3:research0036.1 doi:10.1186/gb-2002-3-7-research0036 |
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