I used Deseq2's Variance Stabalizing Transformation to normalize 16S amplicon otu table. Unlike other users, I have no negative values in my final dataset. Further, I have no 0s in the dataset and, after comparing the transformed otu table to the raw data, I noticed that all of the otus that were 0 in the raw data now have a consistent integer (1.015063211).
Is there underlying code in the VST function that adds a constant integer to all samples? Would it be appropriate to convert all cells with this integer to 0? I'm interested in determining which otus are shared among my treatments, but right now I can't do this because I have no 0s in my dataframe (e.g. can't compare presence/absence across the samples).
Code for transformation: bact.p.deseq=phyloseqtodeseq2(bact.p, ~X.SampleID) vsd<-varianceStabilizingTransformation(bact.p.deseq)
Thanks for your help!