I have a quick question. I have a metadata containing burnt and unburnt site and fire dates… I looked at all my data and performed alpha and beta diversity to compare burnt and unburnt sites, but I want to look at only the burnt sites, specifically the fire dates.
My question is, I have filtered my data to show only the burnt sites, but I am confused on the next steps.
Since I am starting with a new table.qza, which I then turn to a .qzv file, do I have to do the phylogeny tree again prior to calculating alpha and beta diversity, and or will the command automatically know to only look at those samples which I have in the new, filtered table?
To do alpha and beta diversity analysis, I determined a new sampling depth, based on the new table, is this correct?
Is there a way for me to do a PCA instead of a PcOA, or should I just export the data and use it in R-studio?
I have been running the analysis with the Metadata I used for when I analyzed all of my samples. Am I supposed to trim this as well, or is this fine? When I automatically get a message listing all the unburn samples and saying they were not included in the analysis.