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Analyses of statistical correlation between the datasets were performed using the GWR method as described above.
ML analyses of each datasets were performed using RAxML 7.0.3 (Stamatakis et al. 2008), with the GTR + Γ model of sequence evolution selected and the option of a rapid bootstrap analyses (1000 replicates) and a search for the best-scoring tree in a single program run.
Separated gene expression analyses of these two datasets were performed using standard methods: RMA algorithm [45] was used to normalize data within each of the experiments.
ii) After ensuring a normal distribution of α, linear regressions through the cross-sectional and longitudinal datasets were performed using a random-effects GLS regression model with infant-specific intercepts adjusted for sex and weight at the measurement.
Analyses of the resulting micro-CT datasets were performed using the aforementioned software packages.
Comparisons between two datasets were performed using t-tests or Mann Whitney U-tests.
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Initial analysis of the datasets was performed using the Agilent ChIP Analytics software (version 1.3.1) to average both replicates as previously described [36].
Normalization of the datasets was performed using an invariant-set approach.
Analysis of our MeDIP-seq datasets was performed using the Bayesian deconvolution algorithm called BATMAN [ 22].
Analysis of the 'omics-based' datasets was performed using multivariate and correlation analysis.
Similarity structure on metabolic enrichment characteristics across datasets was performed using cluster analysis.
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