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gsea_obj.enrichment() error #184

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WeiQin2001 opened this issue Oct 9, 2024 · 2 comments
Open

gsea_obj.enrichment() error #184

WeiQin2001 opened this issue Oct 9, 2024 · 2 comments

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@WeiQin2001
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test_adata=ad[ad.obs['celltype'].isin(['T-GO01','T-GO05'])]
dds_meta=ov.bulk.pyDEG(test_adata.to_df().T)
dds_meta.drop_duplicates_index()
print('... drop_duplicates_index success')

treatment_groups=test_adata.obs[test_adata.obs['celltype']=='T-GO01'].index.tolist()
control_groups=test_adata.obs[test_adata.obs['celltype']=='T-GO05'].index.tolist()
dds_meta.deg_analysis(treatment_groups,control_groups,method='ttest')

-1 means automatically calculates

dds_meta.foldchange_set(fc_threshold=-1,#-1代表自动计算FC阈值
pval_threshold=0.05,
logp_max=10)

pathway_dict=ov.utils.geneset_prepare('genesets/WikiPathway_2021_Human.txt',organism='Human')

rnk=dds_meta.ranking2gsea()

gsea_obj=ov.bulk.pyGSEA(dds_meta,pathway_dict)

enrich_res=gsea_obj.enrichment()

the following error can be found:
image

@Starlitnightly
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Thanks for your issue, i have fixed it in the latest version

@WeiQin2001
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Thank you!!!!!!

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