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ValueError: Unable to determine gene collection

Open tingxie2020 opened this issue 1 year ago • 4 comments

I receive the error message,

ValueError: Unable to determine gene collection. Please make sure the input dataset specifies either HUGO gene symbols or Entrez gene ID's.

W1_1.var.head() gene_ids feature_types highly_variable means dispersions dispersions_norm n_cells mt rb n_cells_by_counts mean_counts pct_dropout_by_counts total_counts Mrpl15 ENSMUSG00000033845 Gene Expression False 0.523846 1.410226 -0.317858 364 False False 364 0.125276 76.815287 196.682587 Lypla1 ENSMUSG00000025903 Gene Expression False 0.496954 1.360324 -0.604688 356 False False 356 0.117622 77.324841 184.666626 Tcea1 ENSMUSG00000033813 Gene Expression False 1.178549 1.267944 -0.668772 814 False False 814 0.410102 48.152866 643.860168 Atp6v1h ENSMUSG00000033793 Gene Expression False 0.555859 1.411481 -0.310645 389 False False 389 0.138000 75.222930 216.659286 Rb1cc1 ENSMUSG00000025907 Gene Expression False 1.298682 1.432109 0.011839 838 False False 838 0.449731 46.624204 706.077637

the gene_ids should be Entrez gene ids? I change the column name gene_ids to Entrez gene IDs or Gene stable ID or Entrez gene ids, but didn't work. or what code should I use to map the gene ids to Ensembl BioMart (http://useast.ensembl.org/biomart) ?

Thanks Ting

tingxie2020 avatar Aug 18 '22 19:08 tingxie2020