W too high and interpretating results from collapsed/feature table

Hi João and happy 2022!

To detect likely differences in abundance, ANCOM is testing for significant differences in ASV ratios between groups. For each ASV, the number of "successful" tests like that is called W. This means that the maximum W equals the number of ASVs in your table minus 1, in your case 612 - 1 = 611 for the ASV table and 203 - 1 = 202 for the collapsed table. This also means that W values higher than in the tutorial are nothing to worry about and, in fact, you have taxa in your data set with significant differential abundance (even reaching maximum W).

Regarding the x-axis, I only see negative and positive values (the classical volcano crater shape) when I compare exactly two groups. If I compare more than two groups, all clr values are positive, which is also what you see, so I think it is normal. I think the values are made positive during the calculation, but someone else may know why exactly that is.

You may find the following threads useful:

I hope that cleared some of your concerns!

2 Likes