Assistance Needed: Error with imt_gsea - Unexpected Keyword Argument 'perm_index

[xiaobeiLiu]

Hello, when running 'imt_gsea', I encountered an error: 'TypeError: gsea() got an unexpected keyword argument 'perm_index'.' I've tried various methods but still can't resolve it. Can you help me? The code is as follows:

(transcriptomics) C:\Users\96516>imt_gsea --input D:\project\output\Imt_5-HT2A_mean_bmax_pls\pls_analysis.pkl --geneset lake Traceback (most recent call last): File "_ctypes/callbacks.c", line 232, in 'calling callback function' File "D:\Aanaconda\envs\transcriptomics\lib\site-packages\llvmlite\binding\executionengine.py", line 171, in _raw_object_cache_notify def _raw_object_cache_notify(self, data): KeyboardInterrupt Traceback (most recent call last): File "D:\Aanaconda\envs\transcriptomics\lib\runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "D:\Aanaconda\envs\transcriptomics\lib\runpy.py", line 85, in _run_code exec(code, run_globals) File "D:\Aanaconda\envs\transcriptomics\Scripts\imt_gsea.exe\__main__.py", line 7, in <module> File "D:\Aanaconda\envs\transcriptomics\lib\site-packages\imaging_transcriptomics\script\imt_gsea.py", line 63, in main gene_limit=parsed.max_genes) File "D:\Aanaconda\envs\transcriptomics\lib\site-packages\imaging_transcriptomics\transcriptomics.py", line 300, in gsea gene_limit=gene_limit) TypeError: gsea() got an unexpected keyword argument 'perm_index'

[alegiac95]

Hi,
did you run the correlation analysis with one version of the toolbox and then upgraded before running the imt_gsea? it seems to me that the issues you're encountering are due to this, probably.

You can try and re-run the entire pipeline with the same toolbox version and the errors should disappear