Additional file 9 of Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing

Additional file 9: Table S8. Table further describing heatmap in Fig 4. A table was created to mirror the heatmap in Fig 4 in order to further describe the values being represented in the heatmap visualization and calculate number of methods replicating a particular DA signature. Table rows and columns are ordered to match Fig 4. Values for mean relative abundance ratios and mean relative abundances of each taxon in dataset 1 (MRAR_1 and MRA_1) and dataset 2 (MRAR_2 and MRA_2) from the heatmap in Fig 4 are shown. For each method column, cells are labeled to show what DA signature replicated ("Replicated") or did not replicate ("-") instead of the actual values used for generating the heatmap (1 and 0 respectively). Calculations for the number of methods a DA signature was replicated by are located at the right most column of the table. Only taxa that had at least 1 method replicate it's DA signature are included in the table. Heatmap and hierarchical clustering is based on method results when performed on filtered data (excluding taxa found in < 10% of samples). KW: Kruskal-Wallis; GLM: generalized linear model; CLR: centered log-ratio transformation; TSS: total sum scaling; rCLR: robust CLR with matrix completion using OptSpace algorithm; TMM: trimmed mean of M-values; GLM NBZI: generalized linear model assuming negative binomial distribution with, or without, zero-inflation; RLE: relative log expression.