highly_variable_genes - issue

Hi there,

While running sc.pp.highly_variable_genes(adata.X) I got the following error:

AttributeError: X not found

I then ran sc.pp.highly_variable_genes(adata) and got the following:

ValueError: Bin edges must be unique: array([nan, inf, inf, inf, inf, inf, inf, inf, inf, inf, inf, inf, inf,inf, inf, inf, inf, inf, inf, inf, inf]). You can drop duplicate edges by setting the duplicates kwarg

The older sc.pp.filter_genes_dispersion(adata.X) works fine.

Do you know how to fix this?

Thank you!

Info: scanpy==1.3.4 anndata==0.6.13 numpy==1.15.3 scipy==1.1.0 pandas==0.23.4 scikit-learn==0.20.0 statsmodels==0.9.0 python-igraph==0.7.1 louvain==0.6.1

[kanefos]

I have an AnnData object whose .X matrix has been transformed by size factor division, +1 and log. Subsequent sc.pp.highly_variable_genes(dataset, flavor='cell_ranger', n_top_genes=1000) yields the ValueError: Bin edges must be unique: ... You can drop duplicate edges by setting the 'duplicates' kwarg error discussed above. Transformation to a sparse matrix did not alleviate the error, and neither did any other solutions suggested.

Edit: However! While I could not get flavor='cell_ranger' to work on the data I normalised myself, flavor='seurat' has worked okay. Therefore, I recommend people also encountering this error to stick with this second flavour, because as I understand it they utilise a similar methodology.

[Koncopd]

Hi, could you please try

sc.pp.log1p(adata)
sc.pp.highly_variable_genes(adata)

As highly_variable_genes expects logarithmized data.