I am a new user of Qiime and I have a question regarding how I can compare the difference in urine microbiome composition between three timepoints(before, during and after radiation therapy)of a single patient. Below is what my metadata looks like.
Would it be possible to treat each subject as a single "experiment" and see if there's a microbial difference among TP01, TP02, and TP03? If so, are there any recommendations of what method fits the best in this situation?
Sorry if this question is too general but any type of recommendation is appreciated! Thanks!
Your specific cohort sounds a lot like the animal model used in the pd-mice tutorial. In that tutorial, they investigate a series of timepoints from the same individual, and I think you could adapt that method to your data set.
Let us know if you have any questions about these tutorials or how to get started.
