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All sequences were checked for cross-contamination via ViroBLAST [40] against published and local databases, and by observing that sequences from each subject clustered separately from every other subject in a Jukes-Cantor phylogenetic tree calculated in Seaview [41] using an alignment of all sequences from all subjects.
Within each cell type, cell lines derived from the same subject clustered more closely together than to the cell lines from different subjects.
The subject clustered nature of the aberrant data measured from the automated machine S suggests that the device was not properly fitted or functioning for these particular subjects and behoves further investigation.
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V1-V3 sequences from all subjects clustered with subtype B reference sequences.
Multidimensional scaling analyses based on pairwise IBS showed that, apart from some outliers, all subjects clustered closely with HapMap Asians.
Regression techniques that take clustering into account [ 3- 6] are frequently used in cluster randomized trials and in etiologic research with subjects clustered within e.g. neighborhoods or countries.
Principal components analysis showed that C. leptum from most of the control subjects clustered discretely to one side whereas C. leptum from CD and UC patients clustered separately.
Analysis of protein abundances showed that the majority of samples from the longitudinally-studied individual subjects clustered together in the analysis of overall protein abundances.
The subjects clustered according to their periodontal health status, with the periodontitis and control subjects being clearly-separated in the dendrogram; with the exception of only two subjects: H5 and P7.
If a subject is part of a cluster (a joint or "meets with" subject), the clustered subject numbers will be appear in the "Part of Cluster" column.
Of note is that healthy control subjects cluster together at the left side of the graph.
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