Detected zero variance balances while performing "gneiss ols-regression"

[dheeman00 (Dheeman Saha)]

MiSeq_data_v3_table_min_8_feature_filtered_table.qzv (739.7 KB)

MiSeq_data_v3_table_min_8_feature_filtered_table.qza (489.1 KB)

Hi User

I am constantly getting an error while performing qiime gneiss ols-regression. "Detected zero variance balances - double check your table for unobserved features". Can anyone give me some suggestion now I can get rid of the obsolete features?

I used the following command:

qiime gneiss ols-regression
--p-formula "Nitrogen_Month"
--i-table Reduced_Features/MiSeq_data_table_min_8_feature_filtered_table_balances.qza
--i-tree Reduced_Features/MiSeq_data_table_min_8_feature_filtered_table_hierarchy.qza
--m-metadata-file Inputs/MetaData_MiSeq.txt
--o-visualization
Reduced_Features/MiSeq_data_table_min_8_feature_filtered_table_regression_Nitrogen_Month.qzv

I am attaching the actual reduced feature file that is been used to generate the balance and hierarchy files.

[thermokarst]

Hey there @dheeman00 - just wanted to let you know we are looking into this issue right now, but it might be a few days before you hear back from someone. Stay tuned!

[mortonjt (Jamie Morton)]

@dheeman00, looks like you will need to filter out those zero-variance features. I'd take a look at the qiime feature-table filter-features command

There are a couple of posts that discuss this problem in more detail

Integer division or modulo by zero Error

Hello, After running gneiss I identified two outliers by looking at the residual plot and also at the proportion plot. I wanted to remove them from the analysis because they are quite different values from the rest so I filtered those two samples from the table with: qiime feature-table filter-samples --i-table f-table.qza --m-metadata-file Mapping-file.tsv --p-where "SampleID IN ('1157B_FR900_T4', '1162B_FR900_T2')" --o-filtered-table gf-table.qza and then rerun gneiss, but when I run the re…

Gneiss zero balance error

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-visualization regression_summary.qzv Error: Detected zero variance balances... Balance table summary: no zeros (attached) feature-table_summary.txt (7.8 KB) I explored both feature table (prior to g…

[dheeman00 (Dheeman Saha)]

@thermokarst Thank you for looking into the issue. Just a query. Is it a sort of a flaws in the qiime 2 platform.

[dheeman00 (Dheeman Saha)]

Hi There

Thank you for your post. In the second suggestion you have mentioned that there some values of singleton and doubleton. Is it possible to know how I can identify them form my dataset. I could not upload the balance file as it is bigger than the file uploading limit. But some suggestions will be helpful.

MiSeq_data_table_min_8_feature_filtered_table_hierarchy.qza (342.0 KB)
MiSeq_data_table_min_8_feature_filtered_table_composition.qza (581.3 KB)

[dheeman00 (Dheeman Saha)]

Hi @thermokarst and @mortonjt

Thank you for your suggestions. I was able to resolve the issues. I figured out the issue was not that complicated just proper explanation was missed out, which you guys have provided.