ANCOM result volcano plot clr F-statistic calculation formula

ancom
(Josh Hyungyum Kim) #1

Hi,

I’m conducting differential abundance testing with ANCOM and have a question with the clr F-statistic calculation. I’ve checked the forum and found good explanations and intuitions regarding negative F-statistic with only 2 groups, effect size perspective of X-axis, percentile abundance interpretation, and W-statistic hypothese testing.

For me, however, the formula of clr F-statistic calculation (more than 2 groups case) is still sketch even though I somehow understand it’s meaning and intuition. Since it’s not explicitly mentioned in original ANCOM paper and its supplemental material, I hope one of the devs here could provide it’s implementation to qiime2.

Could anyone explain this in terms of F-test with good annotations like @mortonjt did in here?

Thanks in advance,

Josh

1 Like

(Jamie Morton) #2

We wanted to provide a way to visualize something that looks like a volcano plot with multiple categories.

If you have just 2 categories, easy – you just take the difference.

If you have more than 2 categories, then what would you do?
The easiest approach would be to compute something that looks like the F-statistic as a proxy for the differences across groups.

2 Likes