Question: Error in converting seurat object to anndata class
gravatar for Duckula
9 months ago by
Duckula20 wrote:

Hi everyone, I would like to convert my seurat object to an anndata format and for that I am using the following code

Convert(from = Geissmann_Seurat,
        to = "anndata", 
        filename = "Seurat_object_for_python.h5ad",
        chunk.dims = "auto",
        overwrite = F,
        display.progress = T)

But I receive the following error:

Error in py_call_impl(callable, dots$args, dots$keywords) :

ValueError: Variables annot. var must have number of columns of X (23169), but has 0 rows.

Is something wrong in my seurat object or does anyone has an idea what can be the source of the problem?

Thanks alot

R rna-seq seurat python • 622 views
ADD COMMENTlink modified 9 months ago by Biostar ♦♦ 20 • written 9 months ago by Duckula20
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