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zhengrongbin / MEBOCOST

A python-based package and software to predict metabolite mediated cell-cell communications by single-cell RNA-seq data
BSD 3-Clause "New" or "Revised" License
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Error in infer_pathway #27

Closed aboutfanfan closed 1 month ago

aboutfanfan commented 4 months ago

Thanks a lot for your package MEBOCOST! However, when I run the module "Inference of pathway to the communications", there are some error(picture is attached) . Could you give me some advice to deal with this problem?

AttributeError: module 'numpy' has no attribute 'float'. np.float was a deprecated alias for the builtin float. To avoid this error in existing code, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

I would also like to ask two small questions: a. Which reference signal pathway gmt file is used for pathway inference? I did not see this part mentioned in your article. b. Is it possible to compare the differences in pathways/metabolites/sender ~ receiver under different conditions?

Thank you!

image
zhengrongbin commented 4 months ago

Hi Thanks for your interest in mebocost. The error seems to me due to the numpy version problem. Please check your numpy version, probably you need to downgrade to a lower version.

answers to your questions: a. Which reference signal pathway gmt file is used for pathway inference? I did not see this part mentioned in your article. Anwser: it is KEGG pathways.

b. Is it possible to compare the differences in pathways/metabolites/sender ~ receiver under different conditions? Anwser: unfortunately, it does not support analyses for different conditions. We are actually developing the pathway analysis module, we will consider to enable it. Thanks for the question.