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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
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Microbiome

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