normalization in QIIME2

[arlandan]

Continuing the discussion from How to select a Sampling-depth:

Hi @Mehrbod_Estaki,
I found a post with your comments. Very helpful. You mentioned that only rarefying was available at the time the question was asked. I just wanted to know if normalization still not available in QIIME2? Thank you!

[Nicholas_Bokulich]

Hi @arlandan,
Yes, different normalization methods are implemented, but it depends on what type/where you want to use it. Please see this recent discussion for more details:

Normalization for microbiome 16s sequence analysis

The way I understand things, normalization (such as in DeSeq2, EdgeR, etc.) serves two purposes: 1) Model the "real" abundance in the original samples from the read counts, 2) Make the abundance distributions conform to the needs of statistical analysis by removing heteroskedasticity, dependence, dispersion, etc. It has been stated many times here that it is very difficult to reproduce the fold-change you get from DeSeq2 by extracting the normalized counts, but you can come close. Taken at face…