I am working on my thesis project and I have various objectives within my project that I ran these three tests on. For example Objective 1: 3 hives in the same location. However, I am getting very different results for the three different tests and its makes summarizing the results difficult as well as I am having a hard time understanding. I will attatch some fiels iwth what I am seeing between the different tests. I was just wondering if someone could help me understand why I ma seeing the results that I am. I will also attach my metadata file.
So basically this is what my results are telling me: Following the PCoA analysis for Agrarian Hive 1, PERMANOVA results indicated a significant difference between groups (p-value = 0.002), confirming distinct microbial community compositions across the sampling dates and hives. The PERMDISP results showed a significant p-value of 0.032, suggesting that there is significant variation in the dispersion across groups. Pairwise comparisons also showed no significant differences between any of the sampling dates, indicating that while there were some shifts in the microbial communities, the variability between dates was not statistically significant.
Here is my line commends:
qiime diversity core-metrics-phylogenetic
--i-phylogeny BEE.16S.SE.rooted-tree-rep-seqs-dada2.SE.qza
--i-table objective1.qza
--p-sampling-depth 5700
--m-metadata-file sample-metadata-objective1.tsv
--output-dir objective1.core-metrics-results
This part makes sense to me. I would write it up like this:
Figure X: PCoA of Agrarian Hive 1 microbial communities. Significant overall differences (PERMANOVA, p=0.002) and dispersion (PERMDISP, p=0.032) were found across groups, but no significant pairwise differences between sampling dates within this hive.
It sounds like you have a followup question? Perhaps permanova vs permadisp or why pairwise did not pass the significane threshold why while the omnibus test was still significant?
Yes I do wonder why I am seeing those varying results just to get a better idea of my results. Like for instance there are other objectives where PERMANOVA is significant and permadisp and pairwise are not significant. So I am just trying to have a better understanding for putting my document together.
I really do appreciate your help because this has been very informative, but I guess I am still confused on how I would go about talking about this in my document. I know you gave me an example before and well that’s great. I still don’t understand how I would talk about these results and what they mean overall to the whole study. I think I’m having a tough time wrapping my Head around the varying test and the values they’re giving.
