Selection of the most significantly differentially methylated CpG loci between samples was based on (1) a β-value difference of >0.17 [23] and (2) a P-value of <0.0001.
These test-scanned samples were based on spiked samples with a known methemoglobin concentration between 10%and80%0%.
Ward's minimum variance method was used for the construction of hierarchical clusters of the total microbiota probe profiles, while the distance matrix between the samples was based on Pearson correlations.
The association rule between raw data and RNA samples is based on the names of the FASTQ files.
Differential transcription between pathogen-inoculated and mock samples was based on the log2 ratio of the two RPKM values.
The differential expression test between both Evi and control samples is based on the null hypothesis that the expression values of a gene in the samples come from the same distribution, and results in p-values for each gene and sample pair.
Serological status from saliva samples was based on differences between the first and second sample.
Calculation of P-values for comparing the miRNA expression between salt-treated samples and the control sample was based on previously established methods [ 126, 128].
This very large difference is most probably a consequence of the fact that the study sample is based on children between the ages of 10 and 13.
