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write() function error: 'reserved name for dataframe columns' #255
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Running it directly in scvelo works fine
Hence, something is included in Seurat, that triggers that error. Could you please print |
Any updates on this? I'm also having this issue using saving .h5ad files from .h5ad files created using SeuratDisk, exclusively after running scv.pp.moments(adata). The same error does not happen when saving the same .h5ad file after performing additional analysis on scanpy - only after calculating moments within scvelo. |
I'am also having this same issue, running For me it also doesn't work before running scvelo.
raises:
While it works fine with the dataset that VolkerBergen suggested. @VolkerBergen could you maybe specify where you would expect the "_index" entry to be? my AnnData object looks like this in the summary
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I guess, the source of problem is content of the
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OMG!!!!OMG!!!!!OMG!!!!OMG!!!!!PROBLEM SOLVED!!!!!!!PROBLEM SOLVED!!!!!!!THX!!!!!!THX!!!!!!!!!!! |
This works for me for saving the anndata h5ad file, but I got the following message when I plot the dotplot:
I tried to delete the adata.raw:
and now I can save the anndata file, and also it works for the dotplot function. |
If someone is still experiencing an issue with this saving execute also the following: |
recently I encounter this error again after using the original solution for a while, this solved the issue, thanks! |
You are welcome Yuyao! |
Damn man that works....thanks so much....u are a true savior!!! |
BRAVO ! !! |
Oh boy, @mariafiruleva so many thanks!! This command is a little easier to read, for me at least, and seems to do the same thing: adata._raw._var.rename(columns={'_index': 'features'}, inplace=True) |
It works!Thank you very much! |
Hello, I am having an error message when trying to save intermediate results as binary file using
adata.write()
function.The error message seems to happen only when using the Seurat wrapper found here, not when doing the tutorial with 'pancreas' dataset.
See below for R and Python code to reproduce:
Error
Versions:
scvelo==0.2.1 scanpy==1.5.1 anndata==0.7.4 loompy==3.0.6 numpy==1.19.0 scipy==1.5.1 matplotlib==3.2.2 sklearn==0.23.1 pandas==1.0.5
Thank you for the great work and your help.
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