I want to normalize some anndata single-cell object. I filter genes with less than 10 cells before using scanpy and the call the
"normalize" function of the folloeing code:
For some of the matricies it works completely fine but for others I get the following error:
RRuntimeError: Error in h(simpleError(msg, call)) :
error in evaluating the argument 'object' in selecting a method for function 'sizeFactors': error in evaluating the argument 'x' in selecting a method for function 'assay': cannot coerce class "integer" to a DataFrame
Dear MarioniLab-Team,
I want to normalize some anndata single-cell object. I filter genes with less than 10 cells before using scanpy and the call the "normalize" function of the folloeing code:
https://github.com/theislab/scib/blob/main/scib/preprocessing.py
For some of the matricies it works completely fine but for others I get the following error:
The matricies are sparse and of dtype float32.
Maybe you could help me with this issue.
Greeting
Mariam