unable to import s3 and s5 .h5ad objects [GBM spatial paper; Nature Communications 2022]
Opened this issue · 3 comments
Hi, I was interested to look further into the Spatial Transcriptomics datasets from 3 patient-derived GBM samples that was recently published last week in Nature Communication. However, I am running into problems importing 2 out of your 3 datasets. Below are the error codes I receive.
Sample S3
---------s3=sc.read_h5ad('/Users/ShaminiAyyadhury/Research/Projects_Experiments/SmartTherapeuticsGBM/ST_spatial/osfstorage-archive/S3/S3.h5ad')
Traceback (most recent call last):
File "/var/folders/xl/40x0m_b12y5fz7w2hqr_yf480000gp/T/ipykernel_12766/4188748622.py", line 1, in
s3=sc.read_h5ad('/Users/ShaminiAyyadhury/Research/Projects_Experiments/SmartTherapeuticsGBM/ST_spatial/osfstorage-archive/S3/S3.h5ad')
File "/Users/ShaminiAyyadhury/anaconda3/envs/spatial/lib/python3.9/site-packages/anndata/_io/h5ad.py", line 437, in read_h5ad
return AnnData(**d)
File "/Users/ShaminiAyyadhury/anaconda3/envs/spatial/lib/python3.9/site-packages/anndata/_core/anndata.py", line 308, in init
self._init_as_actual(
File "/Users/ShaminiAyyadhury/anaconda3/envs/spatial/lib/python3.9/site-packages/anndata/_core/anndata.py", line 526, in _init_as_actual
self._check_dimensions()
File "/Users/ShaminiAyyadhury/anaconda3/envs/spatial/lib/python3.9/site-packages/anndata/_core/anndata.py", line 1842, in _check_dimensions
raise ValueError(
ValueError: Variables annot. var
must have number of columns of X
(21743), but has 21643 rows.
Sample S5
s5=sc.read_h5ad('/Users/ShaminiAyyadhury/Research/Projects_Experiments/SmartTherapeuticsGBM/ST_spatial/osfstorage-archive/S5/S5.h5ad')
Traceback (most recent call last):
File "/var/folders/xl/40x0m_b12y5fz7w2hqr_yf480000gp/T/ipykernel_12766/137605449.py", line 1, in
s5=sc.read_h5ad('/Users/ShaminiAyyadhury/Research/Projects_Experiments/SmartTherapeuticsGBM/ST_spatial/osfstorage-archive/S5/S5.h5ad')
File "/Users/ShaminiAyyadhury/anaconda3/envs/spatial/lib/python3.9/site-packages/anndata/_io/h5ad.py", line 437, in read_h5ad
return AnnData(**d)
File "/Users/ShaminiAyyadhury/anaconda3/envs/spatial/lib/python3.9/site-packages/anndata/_core/anndata.py", line 308, in init
self._init_as_actual(
File "/Users/ShaminiAyyadhury/anaconda3/envs/spatial/lib/python3.9/site-packages/anndata/_core/anndata.py", line 526, in _init_as_actual
self._check_dimensions()
File "/Users/ShaminiAyyadhury/anaconda3/envs/spatial/lib/python3.9/site-packages/anndata/_core/anndata.py", line 1842, in _check_dimensions
raise ValueError(
ValueError: Variables annot. var
must have number of columns of X
(21743), but has 21643 rows.
Would be grateful if you can look into this and let me know what the issue might be.
Thank you for your time.
Regards,
Shamini A
Sure ... thank you.
Hi, any luck with trying to sort out this issue? I tried to independently convert the Seurat objects to AnnData objects. But it gave the same error as well. I really need to run my scripts on AnnData format as I am using fabian theis's Squidpy package, which runs on AnnData. Thank you.