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

[WangYunHong98]

Hi @alegiac95

I got the same issue.

I used your package (version 1.1.15) on Jupyter Notebook to test. And the script below:

import numpy as np
import imaging_transcriptomics as imt
my_data = np.random.random(50).flatten() 

analysis = imt.ImagingTranscriptomics(my_data, method="pls", 
                                      n_components=1, 
                                      atlas='Schaefer_100', 
                                      n_permutations=1000,
                                      regions="all")
analysis.run(gsea=True)

I got PLS results:

but when running gsea, an issue comes up:

{
	"name": "TypeError",
	"message": "gsea() got an unexpected keyword argument 'perm_index'",
	"stack": "---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
~\\AppData\\Local\\Temp\\ipykernel_64052\\2119373549.py in <module>
      9                                       n_permutations=1000,
     10                                       regions=\"all\")
---> 11 analysis.run(gsea=True)

c:\\ProgramData\\anaconda3\\envs\\transcriptomics\\lib\\site-packages\\imaging_transcriptomics\\transcriptomics.py in run(self, outdir, scan_name, gsea, gene_set, save_res, n_cpu, gene_limit)
    405                 self.gsea(gene_set=gene_set,
    406                           outdir=outdir,
--> 407                           gene_limit=gene_limit)

c:\\ProgramData\\anaconda3\\envs\\transcriptomics\\lib\\site-packages\\imaging_transcriptomics\\transcriptomics.py in gsea(self, outdir, gene_set, gene_limit)
    298                                            perm_index=self._permutation_ind,
    299                                            outdir=outdir,
--> 300                                            gene_limit=gene_limit)
    301 
    302     def run(self, outdir=None, scan_name=\"\", gsea=False,

TypeError: gsea() got an unexpected keyword argument 'perm_index'"
}

Could you help me how to resolve this issue? I appreciate your reply.

[tillandlauer]

Hello, I have a similar issue, no matter whether I run
imagingtranscriptomics --input my_file.nii --regions all --geneset Reactome_Pathways_2024 pls --ncomp 1
or
imt_gsea --input my_file.pkl --geneset Reactome_Pathways_2024

Traceback (most recent call last):
  File ".pyenv/versions/imaging-transcriptomics-env/bin/imagingtranscriptomics", line 8, in <module>
    sys.exit(main())
  File ".pyenv/versions/3.7.10/envs/imaging-transcriptomics-env/lib/python3.7/site-packages/imaging_transcriptomics/script/imagingtranscriptomics.py", line 107, in main
    gene_limit=parsed.max_genes)
  File ".pyenv/versions/3.7.10/envs/imaging-transcriptomics-env/lib/python3.7/site-packages/imaging_transcriptomics/transcriptomics.py", line 351, in run
    self.gsea(gene_set=gene_set, outdir=outdir)
  File ".pyenv/versions/3.7.10/envs/imaging-transcriptomics-env/lib/python3.7/site-packages/imaging_transcriptomics/transcriptomics.py", line 300, in gsea
    gene_limit=gene_limit)
TypeError: gsea() got an unexpected keyword argument 'perm_index'