gneiss dendrogram heat map interpretation

[ssbbrr (Steph)]

Dear all,

I´m just a bit confused on interpreting this dendrogram. I want to know what does y0, y1, y2, y3, y4, y5, y6, y7, y8, y9 means? What does the blue or red indicates? My dendrogram result seems to have no difference between each body site. What could be the reason for this..

Thanks
Steph

[Nicholas_Bokulich]

Hi @ssbbrr,
There is a gneiss tutorial on the QIIME 2 website that I recommend checking out (in addition to the original publication) to get some more info on interpretation (I for one am not the gneiss developer so can only answer some questions about the method in any detail).

@ssbbrr

what does y0, y1, y2, y3, y4, y5, y6, y7, y8, y9 means?

these indicate which features belong to each balance

@ssbbrr

What does the blue or red indicates?

more/less abundant in balance y

@ssbbrr

My dendrogram result seems to have no difference between each body site. What could be the reason for this…

do you expect differences? does permanova indicate a strong significant difference? if not, do not bother with gneiss.

Have you tried using ANCOM? The interpretation is much more straightforward with that method if you have a simple categorical study design (as it looks like you have).

[ssbbrr (Steph)]

Dear Nicholas,

I´m not really expecting significant differences between the three sites: belly, palm and sole. But I was just curious if the sole site would have more abundant taxa compared with the other three sites based on literature. But I guess, the limitation is that I used SILVA database and not a specific database for fungi.. since fungi is mostly found on sole site. That's probably the reason...

Anyways, I haven't tried ANCOM, I have found this website: QIIME2 workflow | CHMI services and I wonder if step 10: differential abundance would be a helpful tutorial? Or do you have a tutorial on qiime2 website that might be helpful with regards with ANCOM?

I´m learning a lot in this forum. Thank you so much for your help.

Best
Steph

[ssbbrr (Steph)]

I think I found the tutorial on the qiime 2 website.

I have a question with the BodySite:

qiime feature-table filter-samples
--i-table table.qza
--m-metadata-file sample-metadata.tsv
--p-where "BodySite='gut'"
--o-filtered-table gut-table.qza

can I change ´gut´, with either belly, palm or sole ? Well yes? as long as it correspond to my metadata.. I will try this out.

[Nicholas_Bokulich]

@ssbbrr

I have found this website: https://chmi-sops.github.io/mydoc_qiime2.html

that looks like a good tutorial, but not an official QIIME 2 tutorial and hence may not be up-to-date with the latest version (I see at least one instance where the commands correspond to an older release of QIIME 2).

Check out our official documentation instead:
https://docs.qiime2.org/2019.7/

there is a gneiss tutorial:
https://docs.qiime2.org/2019.7/tutorials/gneiss/

and ANCOM:
https://docs.qiime2.org/2019.7/tutorials/moving-pictures/#differential-abundance-testing-with-ancom

@ssbbrr

qiime feature-table filter-samples
–i-table table.qza
–m-metadata-file sample-metadata.tsv
–p-where “BodySite=‘gut’”
–o-filtered-table gut-table.qza

can I change ´gut´, with either belly, palm or sole ? Well yes? as long as it correspond to my metadata… I will try this out.

yes, naturally you will need to change these settings to correspond to values that are actually present in your own metadata. However, you may not want to perform that filtering step; e.g., if your goal is to determine which taxa are significantly different between belly and sole then you do not want to filter your table to contain only a single body site. See the filtering tutorial for some more filtering options.

Good luck!