Comments (2)
Thank you for using BEELINE. I was able to reproduce the NaN error in the PIDC output using your example ExpressionData.txt. In the PIDC output I see the following error message for NaN edges:
Gamma distribution failed for Rps3 and Srgn; used normal instead.
I haven't root caused the error and will continue looking into this.
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I haven't found any issues in the way that BEELINE prepares the input or parses the output from PIDC. I believe the error is related to a poor fit of the input to gamma or normal distributions, but I haven't identified how this results in NaN values in the output from PIDC. I recommend following up with the maintainers of PIDC at https://github.com/Tchanders/NetworkInference.jl for further root causing.
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Related Issues (20)
- BEELINE Installation Failure on Windows HOT 2
- Dockerfile compatibility issues with various algorithms, failing to build
- Algorithm SINGE fails to run on Windows - Unterminated quoted string HOT 1
- No general command to run SINGE across different OS
- Add TENET algorithm
- Add the NG-SEM algorithm
- Check the consistency of TFEdges and selfEdges
- Preprocessing for scRNA-seq and scATAC-seq data
- Data download
- Reference networks
- Automatic generation of reference networks
- Faster way of performing AUC Evaluations on larger datasets.
- Python & R versions specified in setupAnacondaVENV.sh are not available HOT 2
- Reduce Disk Space for ExpressionData.csv Copies
- Not able to run GENIE3 and GRNBOOST2 HOT 8
- PIDC method error and not generating any outputs [ERROR: LoadError: MethodError: no method matching setindex_shape_check(::Int64, ::Int64)] HOT 4
- Download single cell datasets from different portals HOT 1
- RankedEdges.csv file missing HOT 2
- where is the tfs+500 and tfs+1000 datasets? HOT 2
- Unable to build and run docker containers HOT 1
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