Fig. 9
From: mbDenoise: microbiome data denoising using zero-inflated probabilistic principal components analysis
DA testing and network analysis on gingival microbiomes of chronic periodontitis. a Visualization of sets of DA species between CP and control groups. Shown are sets detected by t-test, DEseq2, edgeR, metagenomeSeq, and t-test applied to imputed/denoised data (mbImpute, SAVER, and mbDenoise-zinb-cov). We used a FDR threshold of 0.05. b Visualization of sets of DA species between subg and supra sites. c The most common sub-network between CP patients and healthy controls using NetShift. Drivers were red marked. d Spread of drivers for each DA detection method. e Spearman rank correlation between drivers and unique DA species. *Adjusted P values were between 0.01 and 0.05, **Adjusted P values were less than 0.01