Specify W cutoff for anacom?

[mamillerpa (Mark Miller)]

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

[mortonjt (Jamie Morton)]

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.

[mortonjt (Jamie Morton)]

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.

[laurenroukia]

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

[mamillerpa (Mark Miller)]

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?

[mortonjt (Jamie Morton)]

group_significance.py link is fixed!

[mortonjt (Jamie Morton)]

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.

[mamillerpa (Mark Miller)]

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

[ebolyen (Evan Bolyen)]

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!

[serenejiang]

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