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

[Nicholas_Bokulich]

@Mehrbod_Estaki

I’m looking at a simple two group comparison using ANCOM and I’m having trouble understanding the x-axis of the volcano plots. I thought (from reading previous forum posts) that this was the F-statistic but I am noticing a negative value in my outcome and I’m not sure how to interpret that. I didn’t realize F-statistics could ever be negative…

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

@Mehrbod_Estaki

a) Whether the filtering step was ever necessary since there are very few differences between the groups and perhaps this somehow caused the negative values by reducing much of the would-have-been passed sub-hypothesis leading to lower W-values.

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.

@Mehrbod_Estaki

b) If using the filtered table, should I report the absolute F-value or how to interpret the negative value.

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

@Mehrbod_Estaki

c) Overall, what is the recommended information to report from the ANCOM output. The W value is rather uninformative in a sense that is specific to the test and its not really comparable across studies (please correct me if that’s wrong).

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

@Mehrbod_Estaki

The clr-mean-difference as a proxy of effect size?

yes

@Mehrbod_Estaki

Is there some sort of adj.pvalue of the main test somewhere as well?

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

@Mehrbod_Estaki

Lastly, not as important, is it possible to wordwrap the hover-over summaries in the volcano plots into a few lines? As you can see from the unfiltered output from the above example, when the taxonomy string is long, the exact x,y coordinates are cut off from the plots with no other way of recovering that exact info.

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

Thanks @Mehrbod_Estaki! I hope that helps!