# Ancom significance

**URL:** https://forum.qiime2.org/t/ancom-significance/2845
**Category:** User Support
**Tags:** ancom
**Created:** [February 2, 2018, 7:25pm UTC](https://forum.qiime2.org/t/ancom-significance/2845 "2018-02-02T19:25:28Z")
**Posts on this page:** 1
**Showing post:** 6

<div class="post-metadata">

### Author: ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [February 6, 2018, 4:46pm UTC](https://forum.qiime2.org/t/ancom-significance/2845/6 "2018-02-06T16:46:23Z")

</div>

Hi @nricks,  
@Mehrbod_Estaki raises many great points (thank you!), including how the W values are calculated.

> [@Specify W cutoff for anacom?](https://forum.qiime2.org/t/specify-w-cutoff-for-anacom/1844/10):
>
> The W value is just a count of the number of times H0(ij)H\_{0(ij)} is rejected for the ithith species.

Thus W will depend on the number of features, and you cannot really compare W values between ANCOM tests on two different feature tables. Different threshold W scores will be set for each test.

So what you are seeing is not really a "problem". However, what is a problem (as @Mehrbod_Estaki points out) is that in table #2 many many features are significantly different, which is breaking the assumptions of ANCOM.

You might want to check out q2-gneiss; especially since it sounds like you have a potentially complicated experimental setup, gneiss can handle things like multi-factorial experimental designs to determine how species balances differ between groups.

I hope that helps!

---

_[View the full topic](https://forum.qiime2.org/t/ancom-significance/2845)._