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Table 5 Average FPR and TPR by unadjusted analysis on un-normalized/normalized simulated DM OTU tables

From: Powerful and robust non-parametric association testing for microbiome data via a zero-inflated quantile approach (ZINQ)

Sample size = 531         
  Count Rarefaction TSS CSS
α-level 0.05 0.01 0.05 0.01 0.05 0.01 0.05 0.01
  FPR
Corncob 0.0522 0.0115 0.0523 0.0115 - - - -
DESeq2 0.0954 0.0305 0.0951 0.0304 - - - -
EdgeR 0.0588 0.0130 0.0580 0.0133 - - - -
LDM 0.0494 0.0097 0.0493 0.0098 0.0494 0.0097 0.0499 0.0097
Limma 0.0493 0.0098 0.0493 0.0101 - - - -
Linear regression 0.0475 0.0085 0.0475 0.0085 0.0475 0.0085 0.0496 0.0101
MetagenomeSeq - - - - - - 0.1354 0.0552
Monocle 0.9463 0.9296 0.9452 0.9283 0.0481 0.0087 0.0501 0.0102
QRank 0.0489 0.0098 0.0496 0.0096 0.0489 0.0097 0.0491 0.0096
ZINQ-MinP 0.0468 0.0092 0.0468 0.0091 0.0466 0.0090 0.0478 0.0092
ZINQ-Cauchy 0.0522 0.0108 0.0523 0.0106 0.0524 0.0107 0.0523 0.0108
  TPR
Corncob 0.3009 0.1678 0.3000 0.1675 - - - -
DESeq2 0.2210 ∗ 0.1095 ∗ 0.2207 ∗ 0.1093 ∗ - - - -
EdgeR 0.1603 0.0642 ∗ 0.1610 0.0652 ∗ - - - -
LDM 0.1554 0.0646 0.1553 0.0646 0.1554 0.0646 0.2775 0.1530
Limma 0.2923 0.1647 0.2918 0.1646 - - - -
Linear regression 0.1529 0.0611 0.1528 0.0611 0.1528 0.0610 0.2888 0.1619
MetagenomeSeq - - - - - - 0.3165 ∗ 0.1955 ∗
Monocle 0.9610 ∗ 0.9485 ∗ 0.9603 ∗ 0.9476 ∗ 0.1537 0.0616 0.2901 0.1630
QRank 0.2318 0.1156 0.2316 0.1152 0.2325 0.1162 0.2253 0.1088
ZINQ-MinP 0.2419 0.1244 0.2414 0.1236 0.2422 0.1242 0.2391 0.1194
ZINQ-Cauchy 0.2820 0.1511 0.2814 0.1506 0.2819 0.1514 0.2785 0.1449
  1. ∗: power of a method that inflates type I error
  2. Results by the various methods on un-normalized/normalized simulated OTU table generated from the DM models fitted on CARDIA data, including the average FPR and average TPR over 1000 runs according to significance cutoffs 0.05 and 0.01
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Microbiome

ISSN: 2049-2618

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