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mortazavilab / PyWGCNA

PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad415/7218311
MIT License
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functional_enrichment_analysis () #71

Closed bsb2014 closed 11 months ago

bsb2014 commented 11 months ago

My code is

gene_set_library = ["GO_Biological_Process_2023", "GO_Cellular_Component_2023", "GO_Molecular_Function_2023"] pyWGCNA_ASM1.functional_enrichment_analysis(type="GO", moduleName="silver", sets=gene_set_library, p_value=0.05, file_name="GO_silver_2023")

In the log file,

2023-10-24 08:24:13,272 enrichr139917360187568::[INFO ] Run: GO_Biological_Process_2023 2023-10-24 08:24:13,272 enrichr139917360187568::[DEBUG ] Enrichr service using library: GO_Biological_Process_2023 2023-10-24 08:24:14,050 enrichr139917360187568::[INFO ] Save enrichment results for GO_Biological_Process_2023 2023-10-24 08:24:14,630 enrichr139917360187568::[DEBUG ] Generate figures 2023-10-24 08:24:14,630 enrichr139917360187568::[INFO ] Run: GO_Cellular_Component_2023 2023-10-24 08:24:14,630 enrichr139917360187568::[DEBUG ] Enrichr service using library: GO_Cellular_Component_2023 2023-10-24 08:24:15,250 enrichr139917360187568::[INFO ] Save enrichment results for GO_Cellular_Component_2023

I am wondering why functional_enrichment_analysis did not perform GO_Molecular_Function_2023? Thanks

nargesr commented 11 months ago

Hi @bsb2014,

I'm using another package called GSEAPY to do GO analysis. I would suggest checking their website to make sure you’re using the correct gene_set_library name.

If you think that's more like a PyWGCNA problem, please let me know.

Thanks, Narges

bsb2014 commented 11 months ago

It seems that the Enrichr server could not be reached sometimes (https://github.com/zqfang/GSEApy/issues/117).