Multiple testing using significance analysis of microarrays (SAM)
The identification of parameters differentially expressed between treatment arms (unpaired) or within the same participant at different time points (paired) and estimation of the false discovery rate (FDR) was calculated using the siggenes package in R. To decrease redundant parameters of large feature sets, unsupervised parameter filtration was used. Circulating inflammatory markers and untargeted serum metabolomics were filtered to top 75% most varying parameters. Micro and macro nutritional intake were filtered to parameters non-zero in at least 50% of all food logs (95 parameters from 109). Intake for each participant was the average of total food logged during week 0 and week 10 of study. Significance for the SAM was defined as FDR ≤ 0.05 and a q-value ≤ 0.10.