Table 10 Model comparison and alternative approaches (signal in counts, effect size +100%))

DESeq2

(baseline)

0.11 (\(\pm 0.00\))

0.02 (\(\pm 0.00\))

0.17 (\(\pm 0.01\))

0.62 (\(\pm 0.01\))

EdgeR

(baseline)

0.09 (\(\pm 0.00\))

0.01 (\(\pm 0.00\))

0.19 (\(\pm 0.01\))

0.66 (\(\pm 0.01\))

ALDEx2

(baseline)

0.04 (\(\pm 0.00\))

0.01 (\(\pm 0.00\))

0.09 (\(\pm 0.00\))

0.59 (\(\pm 0.01\))

ANCOMBC

(baseline)

0.11 (\(\pm 0.00\))

0.06 (\(\pm 0.00\))

0.10 (\(\pm 0.00\))

0.59 (\(\pm 0.01\))

LinDA

(baseline)

0.10 (\(\pm 0.00\))

0.05 (\(\pm 0.00\))

0.10 (\(\pm 0.00\))

0.59 (\(\pm 0.01\))

Maaslin2 (lm)

(baseline)

0.10 (\(\pm 0.00\))

0.05 (\(\pm 0.00\))

0.10 (\(\pm 0.00\))

0.60 (\(\pm 0.01\))

kruskal_test (strata)

(baseline)

0.12 (\(\pm 0.01\))

0.05 (\(\pm 0.00\))

0.12 (\(\pm 0.00\))

0.62 (\(\pm 0.01\))

oneway_test (strata)

(baseline)

0.18 (\(\pm 0.01\))

0.05 (\(\pm 0.00\))

0.18 (\(\pm 0.01\))

0.65 (\(\pm 0.01\))

Poisson

(llperm)

0.22 (\(\pm 0.01\))

0.05 (\(\pm 0.00\))

0.21 (\(\pm 0.01\))

0.66 (\(\pm 0.01\))

Poisson

(loglik)

0.92 (\(\pm 0.00\))

0.85 (\(\pm 0.00\))

0.14 (\(\pm 0.01\))

0.54 (\(\pm 0.01\))

ZIPoisson

(llperm)

0.29 (\(\pm 0.01\))

0.05 (\(\pm 0.00\))

0.29 (\(\pm 0.01\))

0.70 (\(\pm 0.01\))

ZIPoisson

(loglik)

0.92 (\(\pm 0.00\))

0.78 (\(\pm 0.00\))

0.16 (\(\pm 0.01\))

0.57 (\(\pm 0.01\))

NegativeBinomial

(llperm)

0.23 (\(\pm 0.01\))

0.06 (\(\pm 0.00\))

0.22 (\(\pm 0.01\))

0.69 (\(\pm 0.01\))

NegativeBinomial

(loglik)

0.13 (\(\pm 0.00\))

0.03 (\(\pm 0.00\))

0.18 (\(\pm 0.01\))

0.60 (\(\pm 0.01\))

ZINegativeBinomial

(llperm)

0.29 (\(\pm 0.01\))

0.05 (\(\pm 0.00\))

0.29 (\(\pm 0.01\))

0.70 (\(\pm 0.01\))

ZINegativeBinomial

(loglik)

0.39 (\(\pm 0.01\))

0.10 (\(\pm 0.00\))

0.27 (\(\pm 0.01\))

0.68 (\(\pm 0.01\))