scanpy: Error using rank_genes_groups
Hi,
I have been Scanpy for a short time and I find it really great!
However, I tried recently to use it for differential expression using rank_genes_groups and I could not make it work. I have a single-cell RNA-seq dataset with cell types.
When running rank_genes_groups(adata, groupby="celltype")
, I get the following error:
~/.py3Env/lib/python3.5/site-packages/scanpy/tools/rank_genes_groups.py` in rank_genes_groups(adata, groupby, use_raw, groups, reference, n_genes, rankby_abs, key_added, copy, method, corr_method, **kwds)
374 adata.uns[key_added]['names'] = np.rec.fromarrays(
375 [n for n in rankings_gene_names],
--> 376 dtype=[(rn, 'U50') for rn in groups_order_save])
377
378 if method in {'t-test', 't-test_overestim_var', 'wilcoxon'}:
~/.py3Env/lib/python3.5/site-packages/numpy/core/records.py in fromarrays(arrayList, dtype, shape, formats, names, titles, aligned, byteorder)
632 # populate the record array (makes a copy)
633 for i in range(len(arrayList)):
--> 634 _array[_names[i]] = arrayList[i]
635
636 return _array
ValueError: setting an array element with a sequence
Do you have any idea of what could cause this error?
Thank you
About this issue
- Original URL
- State: closed
- Created 6 years ago
- Comments: 16 (9 by maintainers)
do you have any references on t-test_overestim_var ? I cannot find papers on this test method. what’s the difference from t-test ? @falexwolf
Your observations index contains tuples, which is, kind of weird:
Let me look further…