WebJul 27, 2024 · A total of 585,555 spectra were identified from the six muscle samples used in this study. In total, 20,583 peptides were detected, including 15,279 unique peptides, and 2,540 proteins were identified. We analyzed differentially abundant proteins (DAPs) between LD muscles of donkeys with high (H) and low (L) IMF content. WebNov 1, 2024 · For testing the accuracy of predicting differentially abundant genes, we performed analysis using DESeq2 [29] as described previously [10]. As recommended for microbiome data, geometric means of the data to estimate size factors were calculated, and then the option fitType = “local” was used. MicFunPred showed comparable performance …
Comparative analysis of differentially abundant proteins quantified by ...
WebMar 3, 2024 · The simulation test for how well truly differentially abundant OTUs are recognized by various parametric and nonparametric tests was conducted as in “simulation B” in McMurdie and Holmes , with a few changes. The basic data generation model remained the same, but the creation of true positive OTUs was either made symmetrical … WebAug 9, 2024 · In total, 2666 out of 7289 KEGG Orthologs (KOs) were differentially abundant between gout patients and controls (2260 and 406 KOs enriched in controls and gout patients, respectively; FDR P < 0.05 ... trajanstor
How to calculate differential abundance of taxonomic groups?
WebApr 1, 2024 · The differentially abundant metabolites in the third group (Fig. 2 F) were mainly related to the biosynthesis of secondary metabolites, flavonoid biosynthesis, and … WebMay 25, 2024 · This was most likely due to multiple factors including an overall increase in the proportion of differentially abundant genera being detected by higher concordant methods, a large decrease in the proportion of differentially abundant genera of lower concordant methods such as baySeq (− 0.6 in both datasets) and edgeR TMM (− 0.2 in … WebFeb 15, 2024 · Differentially abundant features of the core microorganisms between the three biological functional zones and between the six different geographically located WWTPs were evaluated. More importantly, relationship between microbial community and environmental variables were established, which is of significance to diagnosis of … trajanumet