ANCOM cutoff determination

Hello QIIME developers/experts,

I have run ANCOM to compare genera distribution across different batches(k = 3). As seen in the attached qzv, g_Chromobacterium has a significantly different distribution. I did a quick visualization with STAMP, and found that the genus is especially abundant in Batch3.

Both g__Barnisiella and g_[Ruminococcus]torques_group appear to have quite high W statistics but are not said to be statistically significant. A quick STAMP barplot visualization would suggest that both are (visually) differentially abundant in Batch1 samples.

I have read through ANCOM discussions in the forum. I also went through the paper and it's supplementary material, but forgive me; I am not from a strong statistical background, and I cannot wrap my head around how W cutoff was determined.

The genera table contains 583 observations. I understand that W stands for the number of subhypotheses being rejected. A score of 399 can be translated as the log ratio for Chromobacterium unequal to log ratio of other 399 genera. From the plot, W cutoff would be in between 399 (g__Chromobacterium) and 336(g__Barnesiella).

Can you tell me how QIIME2/ANCOM compute this cutoff, in layman terms hopefully?

GENUS_ancom_batch.qzv (394.0 KB)


Hi @ZarulSaurus, that is a very good question - something that may be more appropriate ask either the first author or the corresponding author of the ANCOM paper.

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