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PanicException: called Option::unwrap() on a None value #193
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I experience the same kind of Error in a different case. This is the trace:
I use the gsea method like this:
I think the problem is likely that my input dataframe looked like the one below. When preprocessing the data I normalised by z-score, so I had negative values. And if the class mean is negative taking the log2 for calculating the ranking by using log_2_ratio_of_classes won't work. This was obviously an error on my part but maybe this Error could be caught in some way, so it doesn't break the python code.
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I am getting the same error when using the Here is my invocation:
Here is the error message from
Here is the output from using
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@gouinK, you could share the ranking list with me if you don't mind? |
The same problem to me in PyCharm and Jupyter-lab. Don't know how to fix it. But run |
This happened for me using |
I have the same problem with: Run GSEA analysis
The normalize count matrix is this one: Out[4]: [30024 rows x 66 columns] |
@victorsanchezarevalo , would you mind sharing me with your input data frame ? I can't debug only with limited information |
Sure, I am trying to upload the file but it is too big. Could I use wetransfer? Could you provide me an email, please? |
@victorsanchezarevalo you can send me via fzq518@gmail.com. or downsample the file |
Setup
I am reporting a problem with GSEApy version, Python version, and operating
system as follows:
Expected behaviour
I'm running gsea step after converting mouse genes to human genes from my single cell data matrix.
Actual behaviour
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