Issues with Selecting Variable Genes

pinellolab / STREAM

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data

http://stream.pinellolab.org

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Issues with Selecting Variable Genes #60

Closed Olivia117 closed 4 years ago

Olivia117 commented 4 years ago

Hello! Thanks for this wonderful pseudotime tool. Being a first time user, I am having difficulties in selecting variable genes using st.select_variable_genes() function. I am reading an anndata (.h5ad file generated by Scanpy) as input.

It says: IndexError: tuple index out of range

Thanks in advance, Olivia

jipeifeng commented 4 years ago

Hi, it can be resolved by anndata.X = anndata.X.toarray(). This issue was caused by the format of expression matrix