Comments (3)
Added a note in the README in d29cbfd
from single-cell-tutorial.
Added a note in the README in d29cbfd
Hi,
Thanks for your reply, I met another problem for the batch correction
data = pd.DataFrame(adata.X)
batch = pd.Series(adata.obs['sample'])
batch = batch.reset_index()
data_cor = c.combat(data=data.T, batch=batch['sample'])
it reports TypeError: data type not understood
, I have tried np.dtype(data)
, also the same error, seems numpy can not recognize the pandas dataframe type? Can you help me? Thanks.
from single-cell-tutorial.
Hi,
This seems to be a different error that is not related to your previous issue. It would be good to make a separate issue for this. I will try to address this elsewhere.
from single-cell-tutorial.
Related Issues (20)
- get the clustering and subclustering results differ from those given in example
- How can we change the plot shape (not only using dot) of UMAP in Scanpy? HOT 2
- executing sc.tl.rank_genes_groups() function on tutorial data provides incorrect results HOT 1
- Scale before calculating gene score, and after regressing out cell cycle ? HOT 2
- List of package versions for the latest version of the notebook HOT 3
- Sparse matrix dimensions HOT 1
- concatenate to main adata object HOT 1
- enviroment install failed HOT 1
- environment installation problem HOT 1
- ValueError: Unknown dtype dtype('uint16') cannot be converted to ?gRMatrix. HOT 4
- AttributeError: module 'pertpy.tools' has no attribute 'Milopy' HOT 2
- Concatenating issue when plotting analytic_pearson_residuals layers HOT 7
- sc.tl.rank_genes_groups , p value question HOT 1
- creating the env in windows
- Too few Duodenum cells HOT 1
- R command throw UnicodeDecodeError HOT 3
- Batch correction with combat causes Jupyter kernel to die HOT 2
- Key Error "base" in section "marker genes & annotation" HOT 4
- Can we also use Seurat v3 v4 or liger in scanpy or python? HOT 7
- sc.tl.rank_genes_groups and pct1 & pct2 output HOT 1
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