Hello, I'm a beginner in bioinformatics. I'm trying to analyze gut microbiome beta diversity using "R". I'm conducting an analysis using weighted UniFrac distance. There's a slight difference between the results from my code and the 3D plots created with QIIME2. I'm using a tsv file downloaded from QIIME2 that contains weighted UniFrac distances. Since the contribution rates of the plot axes differ, I think the data processing is different, but what kind of processing should I apply to this data to get the same results as QIIME2? By the way, I performed FDR correction.
Would you like me to help with troubleshooting the differences between R analysis and the QIIME2 results?
There is a known disprepancy between QIIME 2 and the phyloseq weighted UniFrac implementation. The QIIME versions are tested against hte original pycogent implementations from Cathy Lozupone in 2005 and 2007; Im not sure about the phyloseq tests.