ValueError: cannot reindex from a duplicate axis

[DUAN-GAO]

Hi,when I execute this code :
adata = adata.concatenate(adata_tmp, batch_key='sample_id')
I got below error,
ValueError: cannot reindex from a duplicate axis

could u help, many thanks

[LuckyMD]

Hey! Are you getting this error with the tutorial data or your own data? It looks like you might have a barcode that is both in adata.obs_names and adata_tmp.obs_names. Or otherwise, check your adata.var and adata_tmp.var for columns with the same name.

[DUAN-GAO]

Mr Malte, I used the sample dataset GEO set GSE92332_RAW, but soon after second GEO data read, when it tried to combine with the first GEO data, it told me cannot reindex from a duplicate axis

[onsamoylova]

Any updates? Did you managed this problem? (Same here, with tutorial dataset)

[onsamoylova]

after line:
adata.var = genes
Add:
adata.var_names_make_unique()

[LuckyMD]

Thanks for the solution. I believe it's reported in another issue as well. It is fixed in the latest version which is only available in PR #58 though.

[Lavieenrose123]

Thanks for the solution. I believe it's reported in another issue as well. It is fixed in the latest version which is only available in PR #58 though.

Hi, I performed the code from your latest notebook (1906) but I still encountered the same problem. I found the problem is due to non-unique index of adata.var. Maybe the reason is, I guess, you didn't make the gene_symbol, i.e., the index of adata.var, to be unique for the first mouse cell (code in jupyter cell #5). It seems that you should also add adata.var_names_make_unique() there.

BTW, cound you please tell me why the same gene_symbol shared different gene_id in that dataset? Thanks!

[LuckyMD]

Hi @Lavieenrose123,

This is exactly the fixthat is in PR #58 as mentioned.

BTW, cound you please tell me why the same gene_symbol shared different gene_id in that dataset? Thanks!

I think this occurs as when you map reads to the transcriptome during alignment, you might be aligning to two different transcripts that map to the same gene (e.g., isoforms).