mothur

Pairwise comparison

Hey folks,
i’ve got a question because i’m not completely convinced by some papers that i’ve read…

following a experimental design from a natural bacterial community (16s), we have a sample at time 0 without replication due to the difficulty to recover DNA sequences, and samples at time 7 after a specific treatment with n=3

Would it be possible to perform a pairwise comparison to know about OTU composition related to the respective treatment? in this case, should I consider the average of triplicate samples, for example?

thanks in advance

Hey Allan,
well yeah, if you have one sample in one group and three samples in the other you can either compare the average with the single sample or perform three independent pairwise comparisons and see how does the contrast change (or doesnt). That being said this is not publishable and it will only serve to give you an idea of how to do the future comparisons (establish a pipeline in R for example). I m currently in a similar process where i m reanalyzing samples from an old study (that are nowhere near the desirable sample size) but it is a good practice for when the real data come :slight_smile: