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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')
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:
The text was updated successfully, but these errors were encountered:
Fixed the error of log_init in gsea_obj.enrichment (#184)
bb2c694
Thanks for your issue, i have fixed it in the latest version
Sorry, something went wrong.
Thank you!!!!!!
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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:

The text was updated successfully, but these errors were encountered: