I am using DESeq2 on a project, where I tested various extraction volumes and types and got amplicon data out. So for instance, I have two extraction volumes 100 Liters and 20 Liters and then I have two extraction methods PowerWater and PowerSoil. I want to compare the resulting microbiomes.
So at first I setup my experiment as: equation
~ExtractionType + Volume; then changed it to equation
~Volume + ExtractionType (I am getting basically the same PCA results both ways). I am wondering if I should change it to
~ExtractionType + Volume + ExtractionType:Volume so that I have all possible varieties in the equation?
I also have 2 different sites being tested, but I was going to set up different experiments for them and just pull out one site set up deseq2 and then do the other experiment.
A few other issues I am having, my Volume is being treated as numeric, even when I turned it into a factor, should I change it to be words in order to force it to be a character instead of numeric or keep it as numeric?
Also I need to test the hypothesis that the micrbiome is the same at both Volumes or Extraction methods. Can you please tell me how I would do so in DESeq?
Thank you so much for your time!