Gneiss turorial error

[jackmen]

Hello,

if I am not mistaken then in the tutorial “Differential abundance analysis with gneiss” the example commands have to be corrected from:

qiime gneiss balance-taxonomy
–i-table composition.qza
–i-tree hierarchy.qza
–i-taxonomy taxa.qza
–p-taxa-level 2
–p-balance-name ‘y0’
–m-metadata-file sample-metadata.tsv
–m-metadata-category Subject
–o-visualization y0_taxa_summary.qzv

to

qiime gneiss balance-taxonomy
–i-balances balances.qza
–i-tree hierarchy.qza
–i-taxonomy taxa.qza
–p-taxa-level 2
–p-balance-name ‘y0’
–m-metadata-file sample-metadata.tsv
–m-metadata-category Subject
–o-visualization y0_taxa_summary.qzv

[mortonjt (Jamie Morton)]

Yup - that is correct. The underlying functionality is not affected with this. The reason why we did this was mainly to enable the proportions - you do need to pass in a FeatureTable[Composition] in order to plot this.

Since we are already passing in a FeatureTable[Composition] object, there wasn’t a good reason anymore to pass in a FeatureTable[Balance], especially because it is so fast to compute a single balance.

[jackmen]

Dear Jamie,

thanks for the reply. I think I did not make myself clear. What I ment was, that the tutorial has to be corrected. But thanks for the nice explanation!

[ebolyen (Evan Bolyen)]

Hey @jackmen,

I suspect you are running an older version of QIIME 2. The docs are up to date with 2017.10, where the parameter was updated to --i-table instead of the old --i-balances for the reasons @mortonjt mentioned.

[jackmen]

Dear Evan,

thank you. I think you are right. I thought I spotted a not updated tutorial command but instead it is me who needs to be updated. As new versions keep coming frequently lately, I have missed that there was an update again. But it is great to see that qiime2 is advancing so quickly. I am a fan.

All the best!