Yes, I am trying to see the results of ancombc for the healthy group and the bipolar group. I have successfully accomplished to generate the ancombc calculations and graphic, but the output of the da-barplot only shows the healthy group:
But on the calculation of the ancombc itself it shows that there are a lot of significant genus with p-value < 0.05 for the bipolar group as well (shown as Intercept):
That's why I don't know if I need to recalculate the ancombc for each group separately. I don't understand why the ancombc da-barplot is only showing the results for healthy control.
I think there's some fundamental misunderstanding going on about what ancombc analysis does. Recalculating ancombc for each group separately does not make sense because the analysis is a comparison between your two groups. There is only one comparison, what could it mean to calculate ancombc for each of the two groups? You could switch the reference to be the other level I suppose but the results will not be meaningfully different, just have the opposite interpretation. I'm not sure how feature-table filtering is involved in any way.
The p-values assigned to the intercept have a different interpretation than the p-values assigned to the non-reference level. It's not very informative in this context, I don't believe. If you want to learn more about this I would recommend doing some searching online or in a stats textbook.
According to the article available at qiime2 page of ancombc ( Analysis of compositions of microbiomes with bias correction | Nature Communications, doi:10.1038/s41467-020-17041-7.) "One of the deficiencies of ANCOM is that it does not provide p value for individual taxon". So, is ANCOM-BC like an "upgrade" of ANCOM, that, through a bootstrap procedure to determine the statistical significance of the W-statistic for each taxon, it allows ANCOM-BC to assign a p-value to each taxon?
Anyway, I think the solution to my problem was just a matter of perspective:
When you compare two groups, such as bipolar vs. healthy, and you observe that a particular taxon is "increased" in the healthy group, it implicitly means that the same taxon is "decreased" in the bipolar group, and vice versa. In other words, saying a taxon is increased in one group inherently provides information about its status in the other group when only two groups are being compared. So it is not that the bipolar group was not being considered, it was. But what is happening is that the healthy group is being considered as the "reference" from the taxa represented.
So, given the image below does it mean that all genus enriched on healthy control (i.e. g__Faecalibacterium, g__ER4, g__CAG-41.... ) are depleted on bipolar? And that all genus depleted on healthy control are enriched on bipolar group? Does my interpretation make sense?
So, given the image below does it mean that all genus enriched on healthy control (i.e. g__Faecalibacterium, g__ER4, g__CAG-41.... ) are depleted on bipolar? And that all genus depleted on healthy control are enriched on bipolar group? Does my interpretation make sense?
Sorry for bothering you again , but do you know if there is a way to extract only the y axis of the da-barplot that I uploaded above, i.e. on a .tsv archive?
Since those features are filtered by multiple parameters that are unique to the da-barplot command as far as I know, I don't think so. You could try cracking open the .qvz to see if they're stored in an easy-to-grab format in there.
