Specify W cutoff for anacom?

I’m used to looking at differential abundances in terms of p-values, like you would get from DESeq2 via phyloseq, or from group_significance_Type.txt in qiime 1 core diversity.

Now I’m trying to get used to anacom, based on the qiime 2 tutorials.

Is it possible to set a W value that is considered significant, like you would with alpha/p-value, either during the

qiime composition ancom

or within the web viewer?

If not, does qiime 2 still offer a t-test or anova-based differential abundance plugin?

thanks,
Mark

Differential abundance is a super touchy topic – there are hundreds of tools out there to do this, and all of them have their own set of assumptions and weaknesses.

The threshold for the W value is automatically determined (see ANCOM paper), so the hypothesis rejection process is a bit hidden from the user. So no, you cannot set threshold for the W-value.

We used to support a bunch of differential abundance tests such as t-test, anova in group_significance.py in qiime1. I’ve been a little edge about this, since it is really easy to come up with super simple scenarios where the false positive rate is close to 100% (see this benchmark for an example).

But maybe it may be worthwhile to revisit this and bring this functionality back into qiime2. At the very least - it could provide a baseline for benchmarking new differential abundance techniques.

10 Likes

I forgot to mention. There is actually already a qiime2 plugin that does do the conventional differential abundance techniques.

That plugin can be found here. Its a bit more robust than the techniques found in group_significance.py, since it accounts for the discretized nature of the sequencing counts using a permutation FDR approach.

2 Likes

Could you help clarify the W values. In my data set the null hypothesis is generally rejected, unless the W value is around/above 60. Thus, should I infer that the lower the W value the more likely that species is not normally distributed between my categories?

Thanks

Thanks for the helpful responses.

It looks like you used the same link for the ANCOM paper and for something I was supposed to read about group_significance.py2

Was that intentional?

group_significance.py link is fixed!

1 Like

The W value is essentially a count of the number of sub-hypotheses that have passed for a given species.

Underneath the hood, ANCOM is just running bunch of pairwise tests. Each sub-hypothesis is structured something like follows (for the 2 class case)

H_{0 (ij)}: mean(\log \frac{x_i}{x_j}) = mean(\log \frac{y_i}{y_j})

where x_i denotes the ith species abundances from samples x, x_j denotes the jth species abundances from samples x

and where y_i denotes the ith species abundances from samples y, y_j denotes the jth species abundances from samples y.

The W value is just a count of the number of times H_{0(ij)} is rejected for the ith species.

So if you have 1000 species, and W=60, for OTU k, then H_{0k.} is rejected 60 times. This basically means, that the ratio OTU k and 60 other species were detected to be significantly different across the x and y groups.

31 Likes

Thanks, @mortonjt

I’m excited to try q2_dsfdr, but I don’t see how to install it (much less run it!) I git cloned the repo, and ran the setup script at the top level:

(qiime2-2017.10) [email protected]:~/q2_dsfdr$ python --version
Python 3.5.4
(qiime2-2017.10) [email protected]:~/q2_dsfdr$ python setup.py 
usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
   or: setup.py --help [cmd1 cmd2 ...]
   or: setup.py --help-commands
   or: setup.py cmd --help

error: no commands supplied

Hey @mamillerpa,

I don’t know anything about that plugin, but with setup.py files, you need to run something like:

python setup.py install

alternatively:

pip install .

should also work.

Hope that helps!

1 Like

Hi @mamillerpa Thank you for your interest! The readme has been updated! Let me know if you have any issues with the installation.

4 Likes

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.