Differential abundance analysis for microbial marker-gene surveys
Citations
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2,184 citations
Cites background or methods from "Differential abundance analysis for..."
...An Expectation-Maximization estimate of the posterior probabilities of differential abundance based on a Zero Inflated Gaussian model, implemented in the fitZig method of the metagenomeSeq package [40]....
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...These simulations, analyses, and graphics rely upon the cluster [54], foreach [55], ggplot2 [56], metagenomeSeq [40], phyloseq [32], plyr [57], reshape2 [58], and ROCR [59] R packages; in addition to the DESeq(2) [13], edgeR [41], and PoiClaClu [46] R packages for RNA-Seq data, and tools available in the standard R distribution [60]....
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...We also compare the performance of the GammaPoisson mixture model against a method that models OTU proportions using a zero-inflated Gaussian distribution, implemented in a recently-released package called metagenomeSeq [40]....
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...We would like to thank the developers of the open source packages leveraged here for improved insights into microbiome data, in particular Gordon Smyth and his group for edgeR [41], to Mihai Pop and his team for metagenomeSeq [40] and Wolfgang Huber and his team for DESeq and DESeq2 [13]; whose useful documentation and continued support have been invaluable....
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...It should be noted that we have adopted the recently coined term differential abundance [39,40] as a direct analogy to differential expression from RNA-Seq....
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1,677 citations
Cites methods from "Differential abundance analysis for..."
...The assigned KO tags were normalized by cumulative sum scaling (CSS) normalization, and then a mixture model that implements a zero-inflated Gaussian distribution was computed to detect differentially abundant properties by using the metagenomeSeq package (249)....
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1,371 citations
Cites background or methods from "Differential abundance analysis for..."
...Our extensive simulation studies show that ANCOM outperforms Zero Inflated Gaussian (ZIG) methodology (1) by substantially reducing the FDR and increasing power....
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...However, it is not clear how (or whether) this information is used in the distributional assumptions made in (1)....
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...Furthermore, according to the statistical model given in the middle of page 2 of the online supplementary files of (1), the ZIG methodology appears to implicitly require that the sum of all observed OTUs be a constant, and not a random variable....
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...Lastly, our simulation studies indicate that the ZIG methodology (1) can produce unacceptably high FDRs and hence may not be suitable for comparing the mean taxa abundance at the ecosystem level between two or more populations....
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...Results: We compared the performance of ANCOM to the standard t-test and a recently published methodology called Zero Inflated Gaussian (ZIG) methodology (1) for drawing inferences on the mean taxa abundance in two or more populations....
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1,309 citations
References
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