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We show that both K-Means and Spectral Clustering yield patterns that correspond to well-known functional systems.
PCA followed by hierarchical clustering yield a dendrogram with two major branching domains (red and green branches; Figure 3A).
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Clustering yielded 34,535 orthogroups.
k-means clustering yielded the same set of indistinguishable patterns (50% accuracy, Fig. 2b).
Applying AP clustering yielded 6 telomere clusters for both P. falciparum and S. cerevisiae, consistent with the FISH data.
Clustering yielded 74,659 unigenes with 33,902 consensus sequences grouped into 11,083 distinct clusters and 41,567 singletons (Table 1).
In contrast, Ward clustering yielded a more balanced regionalisation.
"The clustering yields results that match well with previous studies for the innermost and outermost layers, but for layers in between we observe large variability," they say.
Results: Unsupervised clustering yielded several subgroups, or endotypes, of interest.
The PAM clustering yielded an ARI of 0.894.
The clustering yielded 11 distinct groups, which we designated as MLVA complexes.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com