Negative F-statistic values in ANCOM output after filtering low abundant taxa

It looks like you are getting the same results but the axis is flipped. @mortonjt is this normal?

I do not think that filtering is necessary here — ANCOM is intended to handle high-dimensional data like this — but it will increase runtime so is useful.

I'd recommend using the raw values (depending on Jamie's answer above).

You are correct, W is not comparable across studies. I would recommend reporting the clr-mean-difference and W scores for all significant features.


I believe these values already account for multiple testing but maybe @mortonjt would know more.

Thanks! I have added an issue here to track this.

Thanks @Mehrbod_Estaki! I hope that helps!