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k_selection_plot Error: Last 2 dimensions of the array must be square #3
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Update: Just confirmed that I hit the same error running through the sample PBMC notebook without any modifications to the code, so at least it's not something with the input data. HTML of notebook can be found here I'm running python in a Conda environment set up as described in the README.
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Thanks for posting this! I'm looking into it now and will add an update asap. |
Interesting, I created a conda environment following the instructions and ran the PBMC example from start to finish without any errors. I also ran the pipeline on your data (with similar parameters to what you tried) and didn't hit any errors there either (K selection plot below) I'm guessing this must be some kind of software installation or version issue. But its odd because the versions in your conda environment seem to match what I found. The error is happening on the step where the Frobenius norm is being computed
Maybe try replacing it with something like this?
I'm a bit stuck on how to figure out where the discrepancies in the behavior are coming from. |
Thanks for looking into this--I really appreciate it! Not sure why it's behaving differently. I rebuilt the environment and still had the error, but your fix of explicitly calling np.array worked like a charm! I'll push onward and let you know if I hit any other hurdles--thanks again, Dylan |
I hit the same error! Can you tell me how to replace the code? from a python novice. |
update: I rebuilt the environment. The error changed as follows
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Hey there--thanks for developing this! Really excited to explore it, but I keep hitting an error during k_selection_plot
I exported a count matrix (1775 cells in rows, genes in columns) from Seurat (only cells/genes with sum != 0) as a tab-delimited text file. The first few steps seem to work fine
But then I hit an error during the k_selection_plot run:
Any thoughts about what could be causing this? I can't find anything strange with the expression matrix, but maybe I'm missing something.
In case it helps to see the matrix, I've uploaded it to a Google Drive here
I appreciate the help!
David
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