Error in py_call_impl(callable, dots$args, dots$keywords) :
ValueError: Variables annot. `var` must have number of columns of `X` (3000), but has 18224 rows.
Detailed traceback:
File "/nfs/home/mfiruleva/anaconda3/lib/python3.7/site-packages/anndata/base.py", line 672, in __init__
filename=filename, filemode=filemode)
File "/nfs/home/mfiruleva/anaconda3/lib/python3.7/site-packages/anndata/base.py", line 874, in _init_as_actual
self._check_dimensions()
File "/nfs/home/mfiruleva/anaconda3/lib/python3.7/site-packages/anndata/base.py", line 1944, in _check_dimensions
.format(self._n_vars, self._var.shape[0]))
Calls: <Anonymous> -> <Anonymous> -> py_call_impl
The scale.data slot store 3000 variable genes (by default):
Dear sceasy team,
I have Seurat object and I want to convert it to h5ad using assay = SCT, slot = scale.data.
it gives me the error:
The scale.data slot store 3000 variable genes (by default):
I found that the reason is the meta.features dataframe: it contains information for all the genes:
If I run something like this one:
Everything works fine for me.
Best wishes, Maria