Gneiss picking up of meaningful balances

[Manuss_Ponce (Manuel Ponce Alonso)]

Hi
I'm using Gneiss to find relevant differences in microbial composition. I have been trying to understand the methodology pathway, but I'm still a little confuse with some stuff.

When I inspect the balances, why is more important, the p value (signification) or the number of the balance (higher number means worse)? I attach a csv file of the p values (sorted) obtained from the correlation analysis. There are a few significant balances, and I don't known which i should keep (the lowest ynumber?).

Thanks a lot
fdr-corrected-pvalues.csv (25.1 KB)

[mortonjt (Jamie Morton)]

There is a search bar in the qiime2 forums - have you tried to use it and look up all of the issues with the gneiss tag? This question has been answered several times at the point.

Interpretation of gneiss output table

Hello, community! Thank you very much for all the informative discussion, I'm learning a lot from your conversation. Today, I want to ask about interpretation, and how to report output of differential abundance analysis conducted by gneiss. I performed correlation-clustering, ILR transform and linear regression for 3 treatment conditions adjusted for age, sex, BMI (two categories) as formula "~AGE+SEX+BMI+TREATMENT" and got output. I got a question regarding interpretation of coefficient p-va…

Selection Balances with Gneiss

Hello, I am a little confused on the best method to select which balance to use with Gneiss. I created a model and based on the Gniess tutorial I should be looking at the branch length and the p-values from the heatmap. Does that mean I want to select the balance that is the furthest away (which would be y11 on me tree)? But, this balance does not contain any significant p-values for my variables so should be I be choosing the furthest balance that contains significant variables? Though that fe…

https://forum.qiime2.org/t/understanding-gneiss-outputs/5726/7
https://forum.qiime2.org/t/understanding-gneiss-questions-regarding-the-analysis/3244/2

Gneiss usage and interpreting output

I am using the gneiss plugin and have a few questions about its usage and output: Is it possible to have nested factors in the model? For example, if you primarily want to compare balances in two different species but you have multiple samples from different individuals (e.g. four individuals for each species with each individual represented by samples from cecum, large intestine, and fecal), can you nest individuals within species to account for the statistical dependency of the samples from…

Interpretation of gneiss output table

Hello, community! Thank you very much for all the informative discussion, I'm learning a lot from your conversation. Today, I want to ask about interpretation, and how to report output of differential abundance analysis conducted by gneiss. I performed correlation-clustering, ILR transform and linear regression for 3 treatment conditions adjusted for age, sex, BMI (two categories) as formula "~AGE+SEX+BMI+TREATMENT" and got output. I got a question regarding interpretation of coefficient p-va…

[Manuss_Ponce (Manuel Ponce Alonso)]

Hello Jamie,
Thanks a lot for the links and sorry for not to use the search bar. I carefully read all that topics. It was very useful and I think that now I understand quite more about gneiss, but I came across with an unexpected finding, and I'm looking for help:

I plotted a balance (attached below) with hipothetical interest according to regression summary. In the proportion plot, you can see that Bifidobacterium is more presented in patients with LOWER accumulated-score, but it is represented in the numerator half of the graph. Why? I inspected the numerator taxa csv file and it didn't appear. Instead, It appeared in the denominator taxa csv file. This is contradictory for me.

Is Bifidobacterium part of the denominator half of the balance? Then, why is it plotted in the numerator? Is Bifidobacterium more present in patients with low accumulated score values?

Thanks a lot Jamie

y9_accscore_summary.qzv (167.1 KB)

[mortonjt (Jamie Morton)]

Glad that the search bar came in handy.

Looks like Bifidobacterium is in the denominator and it is more prevalent in lower accumulated-score. So that part makes sense. The part that should not be happening is the boundary in the proportion plot where it looks like Bifidobacterium is in the numerator, when it is actually in the denominator.

So it looks like you found a bug, just raised an issue here: https://github.com/biocore/gneiss/issues/275

Not sure when if I’ll be able to get around to fixing it - and not sure if it is even worthwhile at this point given that all of these tools are in the process of being superseded by upcoming interactive plots (see https://github.com/fedarko/rankratioviz). But PRs are always welcome.