I’m using maaslin2 v1.8.0 and am a bit confused with the scatterplots that are output. I am comparing 16S relative abundance data with a continuous variable, and for a particular species, if I just plot the relative abundances with the variable, there is a clear positive correlation.
However, after running maaslin2 without normalization or transformation, setting the variable as the fixed effect and no random effects, and using either the LM or CPLM methods, the scatterplot appears quite different, with a slightly negative, non-significant correlation. I have tried to upload png images of the plots, but am getting an error.
Should I assume my data is getting mixed up at some step, or is there a possible explanation for this behaviour? I’ve tried looking at the “fitted” dataframe, but I’m not sure how to relate it to my original data. Any help is appreciated.