DESeq2 vs. ANCOM results

[Parix]

Hi,

I have performed DESeq2 on my data, and the results seem to differ from that of ANCOM very much. For example, in case of ANCOM, I found 3 features to be differentially abundant, while DESeq identified over a hundred! I was wondering why the results seem to be so drastically different?

[jwdebelius (Justine Debelius)]

Hi @Parix,

DESeq2 makes some assumptions about biomass load that let it side-step compositionality. Those assumptions may be true for RNASeq data, but have been shown to be less valid for microbiome data in recent years, which can lead to a high false positive rate. ANCOM is quite conservative.

If you’re interested, you might check out some papers that have looked at this over the past few years:

• Weiss et al (2017) Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome. 5:27 doi: 10.1186/s40168-017-0237-y
• Morton et al (2019) Establishing microbial composition measurement standards with reference frames. Nature Communications. 10:2719. doi: 10.1038/s41467-019-10656-5
• Gloor et al (2017) Microbiome datasets are compositional and this is not optional. Frontiers Microbiology. 8:2224. doi: 0.3389/fmicb.2017.02224

Best,
Justine