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Table 2 Results in analysis of the MsFLASH data

From: Constraining PERMANOVA and LDM to within-set comparisons by projection improves the efficiency of analyses of matched sets of microbiome data

      p-values for testing the Number of OTUs
      community-level hypothesis detected at FDR 20%
Arm T1 T2 n-set n-sam permanovaFL LDM Wilcoxon DESeq2 LDM
Estradiol 0 4 10 20 0.26 0.25 0 0 0
  0 8 10 19 0.32 0.52 0 0 0
  0 4 & 8 10 29 0.26 0.32 NA 2 0
  4 8 10 19 0.23 0.27 0 0 0
Venlafaxine 0 4 10 20 0.1 0.033 0 0 0
  0 8 10 20 0.01 0.0042 0 0 0
  0 4 & 8 10 30 0.0022 0.0003 NA 0 4
  4 8 10 20 0.72 0.76 0 0 0
Placebo 0 4 18 36 0.99 0.97 0 0 0
  0 8 18 36 0.77 0.74 0 0 0
  0 4 & 8 18 54 0.96 0.86 NA 1 0
  4 8 18 36 0.6 0.59 0 0 0
Treated 0 4 20 40 0.6 0.61 0 0 0
(estradiol + 0 8 20 39 0.16 0.35 0 0 0
venlafaxine) 0 4 & 8 20 59 0.26 0.31 NA 0 0
  4 8 20 39 0.18 0.18 0 0 0
  1. T1 and T2, the time points between which the samples were compared; 0, the baseline; 4 & 8, week 4 and week 8 after treatment; n-set and n-sam, number of sets (women) and number of samples involved in each analysis; NA, the Wilcoxon test was not applicable