Statistics and Data Analysis for Microarrays Using R and Bioconductor, 2nd Edition

Cluster analysis 595

FIGURE 18.17: Linkage types in hierarchical clustering. Left to right: single

linkag e, complete linkage, centroid linkag e and average linkage.

as centroid linkag e or neighbor joining [398] tend to produce clusters that re-

flect more accura tely the struc ture present in the data but are extremely slow.

The complexity of a bottom-up implementation can vary between n

2

and n

3

,

depe nding on the linkage chosen. In the context of gene expression, one should

try to prune as much as possible the set of genes of interest before attempting

to apply a bottom-up clustering with a more complex linkage.

18.3.2.2 Top-down versus bottom-up

In ...