Hi Folks, I am getting the zero balance error when my balances aren't zero... General Info: QIIME version: qiime2-2017.10 Command: qiime gneiss ols-regression \ --p-formula "Species+Soil_new" \ --i-table balances.qza \ --i-tree hierarchy.qza \ --m-metadata-file my-metadata.tsv \ --o-v…

It could be possible that there are zero variance balances. Could you upload your balances or your FeatureTable[Composition]?

Hi Jamie, Thanks for your help. Attached is the composition table. Cheers, Betsy comp_root_n10_nmc_uMnU.qza (1.8 MB)

@balford looks like your table has a ton of singletons and doubletons, which is known to be problematic whenever you run compositional methods (including ANCOM). Could you try to filter out features that have less than 10 counts in the total experiment? If an ASV only appears 1 time, its likely ga…

Hi Jaime, Thanks for the input. I have re filtered the data for N10 (zero balance error) and now N20 (zero balance error- comp table attached). Due to the large number of samples, should I go up to N100? I have a few hundred samples, should I filter for features which only appear in 5 or more sa…

I think that is reasonable - if a feature only present in 5 samples across the entire experiment, you really can't learn much about that feature to begin with. There is just not enough information. I'm looking at your data, and it looks like there are quite a few features that are only present in …

QIIME 2 Forum

Gneiss zero balance error

User Support

gneiss

show post in topic

Home
Categories
Guidelines
Terms of Service
Privacy Policy

Powered by Discourse, best viewed with JavaScript enabled