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The alternative splicing calculation was performed using the definition of splicing index as average log2 transformed relations between expression levels of individual probe-sets (representing individual exons) and transcript clusters (evaluation of gene expression level) [21].
Because our method used the GO data as prior information to form clusters, evaluation measures such as the entropy for assessing the homogeneity of the clusters with respect to GO terms can introduce some bias.
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Algorithms can then be evaluated using classical extrinsic clustering evaluation metrics [52].
When a ground-truth community structure is available, classical external clustering evaluation indices can be used to evaluate and compare community detection algorithms.
To evaluate the optimal number of clusters, we calculate the clustering evaluation object containing Davies-Bouldin index values and find the minimum criterion value.
To evaluate the optimal number of clusters, we create a clustering evaluation object containing Davies-Bouldin index values in Figure 3(E).
In order to evaluate O-HARP, we compared its performance on the genome clustering evaluation data set against a selection of other algorithms.
In classes-to-clusters evaluation, the class label is initially ignored and the clusters are generated.
But since we had a labeled dataset available to us, we adopted the route of classes-to-clusters evaluation.
Cluster evaluation is usually carried out using graphical methods.
Obviously, clustering evaluation is a stand-alone process that is not included within clustering task.
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