I am trying to see if there are differences in diet in our dataset. It appears there may have been some differences at week-0, I am still waiting to hear if week-0 was just the first week measured or actually prior to treatment administration. While waiting for a response from my collaborators, I thought I would try using first distance with a baseline static point to see if diet is driving differences since week-0, even if there were differences at week-0. In the LME results from first distance baseline-week-0, there is no significance by diet, there is significance by week_number and the regression scatterplot shows me only plots at week-4 and week-8 (my two time points since week-0). However, when I run first distances without baseline-week-0, diet, week and diet:week are significant. The regression scatterplot still only plots week-4 and week-8. Why does the regression scatterplot not include week-0? In both cases, my No. groups = 20 as I have 20 mice, and in both cases my group size = 2. But I have 3 timepoints per mouse. If my week_number for one of the sets of observations is = 0, does that mean QIIME will ignore this set? It seems that is not the case or baseline=0 would be the same as non-baseline.
Being relatively new to LME, I may be formatting my input incorrectly and would appreciate any suggestions. Thank you
Below is an example of the baseline-week-0 first distance commands used. Note that the only difference between this and the non-baseline is: "–p-baseline 0 "
Thank you and cheers Nate
qiime longitudinal first-distances
qiime longitudinal linear-mixed-effects
qiime tools export