Open misialq opened 3 years ago
@BenKaehler, did you write that part of the PD Mice tutorial? If so, care to comment?
To clarify, what changed is that the new uniform (default) pre-trained classifier is using the RESCRIPt-processed greengenes database.
The bespoke classifier is trained using the old (raw) greengenes:
[image: image.png]
So two things need to happen:
On Thu, Sep 24, 2020 at 6:15 PM Matthew Dillon notifications@github.com wrote:
@BenKaehler https://github.com/BenKaehler, did you write that part of the PD Mice tutorial? If so, care to comment?
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Bug Description In the course of going through the Parkinson’s Mouse Tutorial, we noticed that when looking at the taxonomic classification results using the classifier retrained with the information about the typical stool sample composition, the species mentioned in the tutorial (B. ovatus) can be found in both sets of results in equal counts. In other words, with the data provided in the tutorial, retraining the classifier does not really improve the classification results with regard to B. ovatus. It seems as if the data originally used to train the first classifier changed in the meantime giving rise to similar results. In this context the tutorial question about the presence of B. ovatus in both results is potentially outdated.
Steps to reproduce the behavior
taxonomy.qzv
andbespoke_taxonomy.qzv
visualizations from the PM tutorialExpected behavior Not sure, but supposedly the original taxonomy result should have less taxons identified as
ovatus
?Actual behavior Both results show the same number of ovatus taxa.
Screenshots from taxonomy.qzv:
from bespoke_taxonomy.qzv:
![bespoke_taxonomy](https://user-images.githubusercontent.com/22281933/94156141-06b4c280-fe80-11ea-915a-d61cec6b2f60.png)
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