Hello!
I'm finally close to the end of my metagenomics analysis, for which I'm trying to perform a differential analysis through gneiss, to get an oveview about differences among samples. I've used ANCOM too, but I'm trying both approaches.
I'm using this tutorial.
As suggested, first, I've performed correlation clustering with qiime gneiss correlation-clustering , and built linear models with balances and the plugin qiime gneiss ilr-hierarchical.
I'm now about to use qiime gneiss ols-regression
In the tutorial, this is the suggested code:
qiime gneiss ols-regression
--p-formula "Subject+Sex+Age+BMI+sCD14ugml+LBPugml+LPSpgml"
--i-table balances.qza
--i-tree hierarchy.qza
--m-metadata-file sample-metadata.tsv
--o-visualization regression_summary.qzv
And this is where I got lost, more specifically, at the exact meaning of that formula. Apparently, the first four terms represent the 'categorial' type columns of my metadata file, but I can't figure out what the additional terms CD14ugml, LBPugml, LPSpgml are and what those letters stand for.
If I try to run the plugin and still include them in the formula, I get:
Plugin error from gneiss:
Error evaluating factor: NameError: name 'LPSpgml' is not defined
Replicate+Site+Soil+sCD14ugml+LBPugml+LPSpgml
I was able to run the plugin with just the columns names of my metadata file, but I'd like to learn more about such terms. What do they represent and how can I customize them?
Thanks in advance!