Alpha/Beta diversity plots and reporting specific samples/groups that show significant differences

[dfitzer1 (David Fitzpatrick)]

Hello Hannah

Thanks for responding

@jphagen

However, looking at your data the replicates may be problematic. For Kruskal-Wallis, and most of the statistical tests in Qiime2, one of the key assumptions is independence across samples. Replicates have inherent dependance. You will need to work around this by creating models that account for dependance.

I am not sure what you mean by problematic. Do you mean they are not independent as they are in triplicate? Would you suggest the 3 replicates for each timepoint be combined? I thought I had read elsewhere that this was not advised.

how to deal with technical replicates

Hi, Ming! Currently I am analyzing a rumen microbiome as well . I am treating rumen fluid samples from different cows as biological replicates. I did not pool DNA in one sample, neither I merge them in my table. To perform any statistical analysis, or to get an overview of microbiome it is better to have replicates, rather than pool them together.

I could be misinterpreting this and your explanation.

Thanks
David