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| ps_* object | What it contains | Taxonomic composition | Alpha diversity | Beta diversity | DESeq2 differential abundance |
|---|---|---|---|---|---|
ps_raw |
Raw imported phyloseq object (integer counts; as imported) | ❌ (not recommended directly) | ❌ | ❌ | ⚠️ only if you also apply sample filtering first |
ps_base |
ps_raw + taxonomy + sample metadata aligned (still raw counts) |
❌ | ❌ | ❌ | ⚠️ only if you also apply sample filtering first |
ps_pruned |
Optional subset of ps_base (e.g., remove unwanted samples by ID/pattern); still raw counts |
❌ | ❌ | ❌ | ⚠️ only if you also apply low-depth filtering |
ps_filt |
Filtered samples (low-depth samples removed) + taxa with nonzero totals; absolute counts | ✅ as a starting point (but plot on ps_rel) |
✅ as the input to rarefaction | ✅ as the input to rarefaction | ✅ as the input to ps_deseq |
ps_rel |
Relative abundance (compositional) computed from ps_filt |
✅ primary | ❌ | ❌ | ❌ |
ps_abund |
Absolute counts after “plotting taxa filter” (e.g., mean rel. abundance > 0.1%), derived from ps_filt via ps_rel |
✅ (if you want cleaner plots) | ❌ | ❌ | ❌ (not recommended) |
ps_abund_rel |
Relative abundance computed from ps_abund (filtered taxa set) |
✅ (clean composition plots) | ❌ | ❌ | ❌ |
ps_rarefied |
Rarefied counts from ps_filt (even depth) |
❌ | ✅ primary | ✅ primary | ❌ |
ps_deseq |
Non-rarefied integer counts from ps_filt + optional count-based taxon prefilter (e.g., total ≥ 10) |
❌ | ❌ | ❌ | ✅ primary |