Microbiome Analysis by Robert G. Beiko & Will Hsiao & John Parkinson

Author:Robert G. Beiko & Will Hsiao & John Parkinson
Language: eng
Format: epub
ISBN: 9781493987283
Publisher: Springer New York

3.Execute npSeq method using the custom run_npSeq wrapper around the npSeq.Main function in the npSeq R package. This also organizes the results into a data.table with taxonomy.

4.Plot the results using the custom function plot_npSeq, shown in Fig. 5.

Fig. 5Volcano plot of npSeq[14] differential abundance multiple-testing results, displayed as in Fig. 3

3.1.5 Differential Abundance Testing with metagenomeSeq2

metagenomeSeq is an official Bioconductor package, with the explicit goal of detecting differential abundance in microbiome experiments with an explicit design. It models metagenome count data using the Zero-Inflated Gaussian (ZIG) with scale adjustment via cumulative sum scaling [23]. Note that other than zero-inflation, this is not a discrete model, with some analytical performance limitations already acknowledged [12]. A better performing modification has been proposed using the zero-inflated log-normal instead.

1.Load metagenomeSeq package

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