I'm trying to compare two datasets. One of the comparisons I want to do is comparing DESeq's basemean of genes across the two datasets. I did a log of the BaseMean and made graphs. I've noticed that the graphs (below) have a gap at the start meaning that there are no genes with below that many FPKM. I don't think there's a filter in my data, and so I don't know why it's the case. Does anyone have any ideas? My code to run DESeq is here.

  CDS <- DESeqDataSetFromMatrix(countData = ReadList, colData = coldata, design = as.formula("~ Condition"))
  CDS <- DESeq(CDS, test = "LRT", reduced = formula0, minReplicatesForReplace = 5 ) 
  FPKM <- data.frame(counts(CDS, normalized=T)) %>%
  rownames_to_column("ensemblID")

Edit: the picture wouldn't load. Graphs show themselves starting at about 1.25 on the X axis and 3 on the Y axis

Note that scaled/normalized counts, as returned by counts(dds, normalized=TRUE), are not FPKM.

You are saying that there is a minimal value for the mean of normalized counts (baseMean) which is larger than 0? This would only happen if you have removed the genes with 0 count from ReadList.