Error in `preprocess()` when loading from anndata about pywgcna HOT 5 CLOSED

if you can send me a subset of your data that would be great (you can email me: [email protected])

from pywgcna.

Hi,

Can you tell me how you make your anndata object? it's maybe because you have a different layer name rather than the default name (X)

from pywgcna.

Thanks for the quick response. The anndata object contained mutliple layers, right:

merged.layers
> Layers with keys: counts, normalized, normalized_jointly

Although if I rename to X, I still get the same error. I also tried to delete all other layers:

merged.layers["X"] = merged.layers["normalized_jointly"]
merged.X = merged.layers["X"]

del merged.layers["counts"]
del merged.layers["normalized"]
del merged.layers["normalized_jointly"]

merged.layers
> Layers with keys: X

wgcna = PyWGCNA.WGCNA(species='mouse', anndata=merged, save=False)
> # loading works fine

wgcna.preprocess()
> # fails as above

Any other ideas? Might be good to know that the anndata object is based on spatial data (Visium).

from pywgcna.

Hi! I have the same issue can I also email?

from pywgcna.

Hi @simonmfr

Please open an issue including the version of PyWGCNA you used, how you made your anndata, and the error you got.

from pywgcna.