DESeq2

[BlueK77]

Hi, I've tried to run "run_deseq2" from microbiomeMarker package and "DESeq" form DESeq2 package with the same data set and with defaults parameters with both packages. I expected to have the same results or at least very similar instead they are completely different. I am working with microbiome data (with many zeros) and now I am wondering which of the two package I should believe. Are the default settings of "run_deseq2" optimized for microbiome data? If so, which are those settings?
Kind regards