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The number of clusters was chosen by examining the dendrogram and based on clinical interpretability and usefulness.
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Examining the dendrogram in Panel C of Figure 3, we observe TopHat2 and Bowtie2 have the shortest distance between gene expression estimates, followed by GSNAP, Bowtie2-G, and Stampy-G, and finally Stampy.
A taxonomic supervised dendrogram was prepared to examine the overall variation in the microbial community of the samples.
Then the community structure is acquired by cutting the dendrogram at the levels corresponding to the maximum modularity.
Jerarca establishes partitions by scanning the dendrogram from the root to the external leaves.
The number of clusters (M) is determined by inspecting the dendrogram.
The ultimate clustering results are obtained by slicing the dendrogram at a particular level.
A total of 28 clusters were produced by cutting the dendrogram at height 0.75.
To further examine the relatedness of the serotype HS∶41 strains from these two geographical locations, a dendrogram was constructed by using the neighbor joining method for pairwise comparisons of the concatenated seven allele sequences (Figure 1).
A dendrogram was constructed on the single channel values both before and after normalization to examine the effect of normalization on the treatment differences.
The ordering is given by the dendrogram which is displayed on the side of the heatmap.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com