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In addition, the calculation speed for the complete linkage method is 3-fold enhanced than that for the k-means method (data not shown).
Since the complete linkage method provides higher modularity, higher speed, and less CVs of cluster size than the k-means method, the complete linkage method is selected for clustering the diffusion map of the PPI network.
To add a layer of security, for an actual implementation of the Bloom filter method the hash functions SHA1 and MD5 should be replaced by a keyed hash message authentication code (HMAC) HMAC-MD5 and HMAC-SHA1 [ 50] with a secret key K. Based on this enhanced Bloom filter method, the implementation of a record linkage method is quite simple.
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The Ward's linkage method was used in this analysis.
Between group average linkage method was applied, and rescaled distance was selected as measurement.
The average linkage method was used to build the dendrogram, which represented the nested correlation structure of all AE events.
A classification scheme using the Euclidean distance for similarity measures and the between-groups linkage method was performed on the normalized data to produce the most distinctive classification where each member within a group is more similar to its fellow members than to any member outside of the group (Guler and Thyne 2004).
The distance matrix was 1-correlation and linkage method was average.
Two typical clustering methods: k-means and completed linkage method are employed to divide the (k-1) dimensional diffusion map into k clusters.
The overall profile of methylation was examined using unsupervised hierarchical clustering where distance matrix was 1-Pearson correlation and the linkage method was average.
Ward's linkage method was performed on Euclidean distances from the standardized aminogram using the JMP 8.0.1 program (SAS Institute Inc., Cary, NC).
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