What the Intercept?

If you have run standard differential abundance tools such as DESeq2, Aldex2 or even my tool Songbird, you may have realized that there is an intercept reported in the output. You may also be wondering how can you interpret this quantity? This may be confusing especially if you are only looking at categorical variables, such as the difference between treatment and control groups.

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Thoughts on reference frames

We just had a paper come out about how to make sense of differential abundance in the context of microbial sequencing data. The basic premise behind this work is that inferring differences (between sick/healthy people for instance) in microbial abundances from sequencing data can be counter intuitive. We confirmed that fluctuations in total microbial biomass is a major confounder, and we have proposed a couple of different solutions.

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