Aldex2 aldex.glm results

[bmpaddy]

Hi! I am trying out the glm run with model matrix to my data. Everything goes fine when running aldex.clr and aldex.glm. However, when I inspect the result data frame, it doesn't return one of the variables in my model matrix. When running aldex.glm.effect, all variables are now included in the glm effect data frame. I am comparing 8 groups/conditions in my data.

[mirpie]

hi,
Not sure if this is what you're referring to, but if I understand correctly you're referring to the fact that one of your conditions is being excluded from the various combinations in the results. This is because Aldex takes the first alphabetical level of each factor in the design and sets it as the "baseline", i.e. all other levels in the factor are compared to that baseline. So for example if I had "GenotypeA" and "GenotypeB" in one condition then I would only "see" results for GenotypeB, which provided stats for differences in taxon abundance as it compares to A (ex. model.GENOTYPEB Pr(>|t|), etc.)