ANCOM v2.1 and ANCOMBC, difference?

[Ivy-ops]

Hi developer,
I am a little confused, what's the difference between ANCOM-BC and ANCOM v2.1?
I have been always using ANCOM v2.1, is it different from ANCOM-BC?

Thanks!!!!

[FrederickHuangLin]

Hi @Ivy-ops,

Thanks for your interest in our methods!

Both ANCOM and ANCOM-BC are methods of differential abundance (DA) analysis and they are handling the same problem, which is to detect the differential abundant taxa. However, since these two methods are based on different methodologies, you will expect slightly different results from them using the same dataset. Based on our simulations, the results shall be pretty consistent.

Additionally, ANCOM-BC is still an ongoing project, the current ANCOMBC R package only supports testing for covariates and global test. Other tests such as directional test or longitudinal analysis will be available for the next release of the ANCOMBC package.

Best,

Huang

[ETaSky]

Same question here, I am also not sure about the fundamental difference between ANCOM-II and ANCOM-BC. They use the same framework to deal with the "three types" of zeros. ANCOM-II (as in Kaul et al. 2017) also has a part to adjust for sequencing depth (eq. 2.3), although that equation may be problematic.
Is it that the reference frame chosen by ANCOM-II and ANCOM-BC is different?

[FrederickHuangLin]

Hi @ETaSky,

ANCOM-II and ANCOM-BC methodologies are not the same. ANCOM-BC only adopts the framework for dealing with the "three types" of zeros from ANCOM-II.

The ideas for testing differential abundance are different.

Best,
Huang

[joshborin]

Hi @FrederickHuangLin, I am wondering if ANCOM-BC is now able to do longitudinal analyses? I did not see it mentioned in documentation, just cross-sectional analysis.

Thanks!
Josh

[FrederickHuangLin]

Hi @joshborin,

Thanks for your inquiry!

ancombc does not support the longitudinal analysis in this version (1.6.2), but it is undergoing a major update that will incorporate longitudinal analysis and more. The update will be published in probably a month.

Best,
Huang