I am really happy you are getting Aldex2 up and running @dgiguer
The results indicate that I don't have a condition defined and the --help vs. the tutorial files are not lining up. There is a divergence between the --help commands vs. the library.qiime2.org tutorial. Here is my code and error (not recognizing the category)
(qiime2-2019.7) pmrubine-u01dx:Gneiss kristinaadmin$ qiime aldex2 aldex2 --i-table filteredtable.qza --m-metadata-file DVSMetadata.txt --m-metadata-column Combined --p-test glm --p-denom iqlr --output-dir FeedAldex2 --verbose
Traceback (most recent call last):
File "/Users/kristinaadmin/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py", line 327, in call
results = action(**arguments)
TypeError: aldex2() missing 1 required positional argument: 'condition'
Plugin error from aldex2:
aldex2() missing 1 required positional argument: 'condition'
In the --help file, I did just those directions. Using the tutorial...I get...(feed=combined)
See above for debug info.
(qiime2-2019.7) pmrubine-u01dx:Gneiss kristinaadmin$ qiime aldex2 aldex2 --i-table filteredtable.qza --m-metadata-file DVSMetadata.txt --p-condition Feed --output-dir FeedAldex2 --verbose
Usage: qiime aldex2 aldex2 [OPTIONS]
Performs log-ratio transformation and statistical testing
Inputs:
--i-table ARTIFACT FeatureTable[Frequency]
The feature table of abundances [required]
Parameters:
--m-metadata-file METADATA
--m-metadata-column COLUMN MetadataColumn[Categorical]
The "condition": this column will be used as an
experimental descriptor to group samples [required]
--p-mc-samples INTEGER The number of monte carlo samples to be used
[default: 128]
--p-test TEXT The statistical test to run
Choices('t', 'glm') [default: 't']
--p-denom TEXT Choices('all', 'iqlr')
The features used to decide a reference frame
[default: 'all']
Outputs:
--o-differentials ARTIFACT FeatureData[Differential]
The estimated per-feature differentials [required]
Miscellaneous:
--output-dir PATH Output unspecified results to a directory
--verbose / --quiet Display verbose output to stdout and/or stderr
during execution of this action. Or silence output
if execution is successful (silence is golden).
--citations Show citations and exit.
--help Show this message and exit.
There was a problem with the command:
(1/1?) no such option: --p-condition
(qiime2-2019.7) pmrubine-u01dx:Gneiss kristinaadmin$
See above for debug info.
So, there is a disparity and I don't know how to resolve this as the github documentation is not great either (same error). I think this is an amazing plugin and I look forward to your feedback.
featureid kw.ep kw.eBH glm.ep glm.eBH