Greetings,
I have three groups of microbial samples (A, B, C), and two different timepoints of sampling (baseline and follow up). Can I use ANCOM BC2 despite these NOT being cross-sectional data? (they are longitudinal, with two different time points).
Thank you in advance.
Hello and welcome to the forum!
I would say, that it depends on the questions you want to answer!
For example, if you want to compare groups B and C to A at time-point 0 as separate analysis, and then compare the same groups at time point 1 as another analysis, and then discuss the differences you can do it in Qiime2.
If you want to perform longitudinal comparisons, you can use Ancombc2 R package, since Qiime2 only wraps cross-sectional designs.
Best,
Thank you for your answer. I have already used ancom bc2 in R for this project. It is just that I am not sure if it is theoretically correct. For example, if this was a standard t test, I would have to use a paired t test to compare baseline and follow up.
As far as I know, Ancombc2 R supports longitudinal design. I am not very proficient with R, but I remember that in their R tutorial they have a separate section for that.
Here's an example using a diet-swap cohort. This sounds very similar to your project!
(I've moved this to Other Bioinformatics Tools because there's not a qiime plugin for ANCOM-BC2... yet!)
Thank you for this example. I have seen this before, but I couldn't find the original study.
Ah, here's the published paper: Fat, fibre and cancer risk in African Americans and rural Africans | Nature Communications
It's part of the microbiome R package / GitHub org (confusing name, I know)
Perhaps this import makes it more clear:
library(microbiome)
data(dietswap) # from the package `microbiome`