Normalization and ANCOM

Hi all,

Is CSS or Deseq supported in Qiime2 yet? If not, is it a good idea to import into Qiime1 to run CSS or Deseq then import back into Qiime2 for downstream analysis? I’d much rather keep all my analysis in Qiime2…

Also, what’s the deal with ANCOM? Can it be used for normalization? From my understanding, it’s used to identify how different the abundances of shared features are across samples, but doesn’t the Taxonomic Analysis step in Moving Pictures Tutorial tell you this? Can someone give me a brief explanation of the major pros and cons? Thanks!

Hi @Alan_Chan,

Normalization methods like CSS or DESeq are not available in qiime2 yet. The choice of doing these outside of QIIME2 and re-importing is totally up to you and your specific questions in mind. Depending on what you plan on doing you might not have to do those at all.

For example, ANCOM (and gneiss) don’t require any normalization as they use log ratios of your composition data (pro!), though they do have certain assumptions of their own which you’ll need to account for (con?). You wouldn’t have to leave qiime2 (pro) but the current version of ANCOM in qiime2 doesn’t allow for longitudinal comparisons and mixed effects models (con) though you can with gneiss, see tutorial here. The taxonomic analysis in the moving pictures tutorial simply provides barplots of your taxonomic composition but doesn’t perform any statistical testing. The barplots are more for exploration purposes. With ANCOM you can actually test for differential abundance of individual taxa across groups.


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