ValueError("Plan shapes are not aligned")

[kkamii]

Hello !

I got this issue when running statistical_analysis method

my code is "cellphonedb method statistical_analysis ../../patient3_meta.txt ../../patient3.h5ad"

I don't know why this type of error occured.

How can i fix it??

help me..

[prete]

Hi @kkamii could you provide your CellPhoneDB and Pandas version (pip show cellphonedb pandas)? That value error usually comes from pandas DataFrame.concat(...) function failing to integrate to DataFrames. Are you using a custom database or the default one (v.2.0.0)?

[kkamii]

hello @prete !

thank you for your answer

I'm using default database v.2.0.0 and I captured my cellphonedb & pandas version

[prete]

@kkamii that looks OK. At what stage of the process you see that error(could you paste the whole output?). Additionally, could you share your meta/counts file with us to troubleshoot his? If you can't, I'd recommend you try reducing the number of cells in dataset (shrinking the cells in your meta or counts) and see if you get the same error.