ANCOM Analysis?

Hi all,

I did my microbiome analysis already using QIIME 2 v 2017.9 but now I want to do some statistical analysis to confirm the changes I am seeing in my taxa box plot. I was wondering if ANCOM analysis will help on this or if you can suggest another test I can use in this case in QIIME2 or even any other tool like R. Basically, what I want to know if which changes in the organisms abundances are significantly different or not across my samples.
A would appreciate any suggestion.

Thanks a lot!

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Hi, I think you already answered your question - you can use ANCOM in q2 to reveal which features are significantly changed

Thanks so much! Wanted to be sure!


Hey again,
In the Volcano Plot, what “W” stands for?


The bigger meaning, the more difference, if I am not mistaking

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Check out the original publication for more details, but here’s a great explanation on this forum: Specify W cutoff for anacom?

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I have another question about the Ancom command. This is what I am trying to run:
qiime composition ancom
–i-table MRE-comp-taxonomy_ResistantStarch_Only65_orderedbytimepoints-l7.qza
–m-metadata-file mapping_file_resistant_starch_only65_orderedbytimepoints_09_07_18_ANCOM
–m-metadata-category Diet_Time_Point
–o-visualization MRE-l7-ancom-Diet_Time_Point.qzv

It worked but in the category I want to be more specific for the analysis and selected only six samples of about 33 samples for the “Diet_Time_Point” category. How can I do that? So far, I am getting the analysis for all the samples in that category and the abundance table is big.

I would appreciate your help!


There is a tutorial “Filtering data”, you can found there how to filter your table according different parameters, including samples.

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Thanks! I looked it and is working.

What is happening if I don’t I Volcano Plot? I am doing something wrong?

Unable to generate volcano plot, please check the ANCOM statistical results (above).


Hey @idapantoja,

You probably need to update your installation, 2017.9 is pretty old at this point. I do remember something about the volcano plot being conditional, but I don’t remember the details, @mortonjt was that the case?

Correct, you may be experiencing an outdated version of bokeh