Open Alice9503 opened 2 weeks ago
I've actually already installed R with the 'qvalue' and 'rpy2' Python package by mamba install -y rpy2 bioconductor-qvalue
before pip install tensorqtl
I can't reproduce these issues with the example notebook. Please try again with v1.0.10.
Description: While running the official TensorQTL example dataset in Jupyter Notebook, I encountered several warnings and errors that seem to impact the successful execution of the example:
Warning:
"Warning: 'rfunc' cannot be imported. R with the 'qvalue' library, and the 'rpy2' Python package are needed."
Frequent Warnings during Permutation Computation:
Upon further inspection, I found NaN values in the cis_df DataFrame specifically in the beta_shape1, beta_shape2, and pval_beta columns, with the following summary:
Request: Could you please provide a list of specific versions (Python, TensorQTL, dependencies, etc.) in a fully functional environment? I will then attempt to replicate the environment locally to test the example.
I've attached the full tensorqtl_examples.ipynb notebook with complete error output for reference.
Thank you for your assistance! tensorqtl_examples_used.zip