Gneiss questions

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  1. You may be able to import those taxonomies into qiime2 artifacts via qiime tool import. Maybe @gregcaporaso can clarify the details on how to do this.
  2. Nope - the main premise behind Gneiss that it is physically not possible to make inferences on individual microbes. We discuss this in detail in the balance tree paper. We try to answer a relaxed form of the question, so that we don't fall into the trap trying to infer which microbes are growing / declining.
  3. The downloaded pvalue coefficients aren't FDR adjusted -- but the visualized pvalues in the heatmap in Visualization Artifact does have FDR calculations. Right now, those pvalues will need to be corrected after download (we can raise an issue for this if we want to add FDR pvalues on download).
  4. That's a really cool idea. We currently don't have an out-of-box solution for this, and I'm not sure what the best way about this is. One possibility is to build two models, a full model and a partial model. For example
    Full model: formula=Sex+Age+BMI+sCD14ugml+LBPugml+LPSpgml
    Partial model:formula=Age+BMI+sCD14ugml+LBPugml+LPSpgml
    Then you'd have residuals for the full model, and residuals for the partial model. This might be able to help you get idea about the residuals due to Age.
    The details would need to be worked out. But if feature is highly desirable, feel free to raise an issue here. Furthermore, contributions via pull requests will be warmly welcomed.
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