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Our approach is applicable whenever a dissimilarity or similarity measure can be defined between samples (see Additional file 1).
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Instead, distance-based non-parametric testing, in which a distance measure is defined-between any two microbiome samples, is usually used to achieve this goal (Fukuyama et al., 2012; Kuczynski et al., 2010a; Wu et al., 2011, 2010; Charlson et al., 2010).
The dynamic image range was defined between 0 and 0.045 for all the samples.
This configuration facilitates the quality control and digital image analysis of the cell arrays as cells included in the analysis can be defined without possibility for sample mixing between array positions.
The Agonal Stress Rating is thus defined as the difference between each sample's distances to the two prototypical patterns, and can be calculated by using different sets of most informative genes, which in turn can be defined by comparing the most extreme samples (see Methods).
Similarly noise samples can be defined.
To investigate the association between gut bacterial communities and obesity, 45 stool samples of participants with a BMI of ≤ 24 were defined as normal samples, and 36 samples of participants with a BMI ≥ 27 were used as case samples.
The standardised difference between the reported sample size calculation and the replicated one is defined by the reported sample size calculation minus the recalculated sample size divided by the reported sample size calculation.
In general, clusters were defined by geographic proximity between sampling localities.
ΔΔCT was defined as ΔCt treated sample − Ct control sample.
(6) o ij = j ' 1 … j ' m − 1 such that d ij ' 1 j < … < d ij ' m − 1 j (7) O D ij = ∑ l = 1 k d ij ' j | j ' = o ijl The WOD methods are similar to the OD method but rely on a weight matrix describing the sample-to-sample dissimilarity, which is the m × m matrix W and is defined by the Euclidean distances between samples as in (8).
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Justyna Jupowicz-Kozak
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