Question: Error in converting seurat object to anndata class
gravatar for Duckula
17 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 • 936 views
ADD COMMENTlink modified 16 months ago by Biostar ♦♦ 20 • written 17 months ago by Duckula20
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1202 users visited in the last hour