Hi! I am just starting to work with ANCOM and gneiss to get some differential abundance data. I have a complicated dataset containing the 16S gene from the V1-V3 region and the V4 region. Within each region I have DNA and RNA. I want to compare everything to see what taxa are over/under-represented in V1-V3 compared to V4 and also between DNA and RNA. My question is what exactly should I do to find out the taxa that are different? I have tried gneiss with gradient clustering by region (I made the data numerical for it). I am not sure if this is appropriate though, or if I should stick to correlational-clustering?
I am also a little confused as to what I should be doing for the ols regression formula. So far I’ve done --p-formula “Treatment+Sample_Day+DNA_or_RNA”
I don’t think the sample day has any impact but, I put it in just in case.
Sorry if this post is too generic, I am just learning all of this and trying to teach myself about balances etc.
Thank you all for your continued help!