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alegiac95 / Imaging-transcriptomics

A package, and script, to perform imaging transcriptomics on a neuroimaging scan.
https://imaging-transcriptomics.rtfd.io/
GNU Affero General Public License v3.0
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error in running imt_gsea with geneset except 'lake' and 'pooled' #23

Open YufeiChenGithub opened 3 months ago

YufeiChenGithub commented 3 months ago

I run imt_gsea in linux command line:

~$ imt_gsea -i ~/cyf/IMAGEGENE/Imt_cth_z_reflect_pls/pls_analysis.pkl -g Allen_Brain_Atlas_up -o ~/cyf/IMAGEGENE/AHBA 2024-06-06 18:07:16,803: Performing GSEA. 2024-06-06 18:07:16,814 Input gene rankings contains duplicated IDs, Only use the duplicated ID with highest value! 已杀死

~$ imt_gsea -i ~/cyf/IMAGEGENE/Imt_cth_z_reflect_pls/pls_analysis.pkl -g GO_Biological_Process_2023 -o ~/cyf/IMAGEGENE/AHBA 2024-06-07 15:22:33,474: Performing GSEA. 2024-06-07 15:22:33,572 Input gene rankings contains duplicated IDs, Only use the duplicated ID with highest value! 已杀死

~$ imt_gsea -i ~/cyf/IMAGEGENE/Imt_cth_z_reflect_pls/pls_analysis.pkl -g MSigDB_Computational -o ~/cyf/IMAGEGENE/AHBA 2024-06-07 15:41:39,947: Performing GSEA. 2024-06-07 15:41:40,067 Input gene rankings contains duplicated IDs, Only use the duplicated ID with highest value! 已杀死

lyhoo23618-csu commented 2 months ago

Hi,

I encountered the same error and failed to adress it. I noticed that the geneste databases, except for 'lake' and 'pooled', need to be fetched from the Gesapy package. Could there be an issue with this package?

Best regards, Hao