A plot of the agglomeration coefficients in the successive steps revealed an elbow at the four-cluster solution.
For example, the agglomeration coefficients identified several possible cluster solutions (i.e. 4, 5, 6, 7 and 8 clusters), which were each subsequently explored with non-hierarchical cluster analyses, following Hair et al. [ 23].
From Figure 5, we can observe some consistent properties that we find during a terrorist attack: the increase in Gini coefficient, the agglomeration of network structure and the decrease in assortativity.
The slurry agglomerates in the diffusion limited agglomeration (DLA) or reaction limited agglomeration (RLA) regime.
Hierarchical clustering was performed after centering of peak expressions using the Ward Agglomeration Algorithm and a distance defined by the correlation coefficient for peaks and an euclidean distance for samples.
The retained features (3,573 total) were then subjected to hierarchical clustering using Pearson's correlation coefficient as distance metric and the average agglomeration method.
The use of clusterStab package showed that the best reliability of the number of clusters was detected when using Pearson correlation coefficient as metric, Ward's method as agglomeration method, and k = 2 clusters.
The 739 genes were then organized by hierarchical clustering, using a function of the Pearson correlation coefficient as the distance metric and the average agglomeration method.
Then, we have performed hierarchical clustering of features based on the absolute value of the rank correlation coefficient (as described in Additional file 6); the agglomeration method used in the clustering was 'unweighted pair-group average' and the correlation threshold was set to 0.9.
Hierarchical clustering of differentially expressed genes was performed using the Cluster software package [ 92], using the function (1 - Pearson correlation coefficient) as the pairwise distance metric and the average agglomeration method.
