Gioele La Manno

Everything looks allright. Are you running on a powerful enough machine? Could this be a memory issue? Could you monitor that while running? Can you check which version of velocyto...

And running the code I wrote above crashes the notebook as well?

I am out of suggestions, try to run the code of the notebook in a script instead. Let's hope it throws an error instead of chrashing... so I can understand...

I didn't mean you had run the code literally as is. I assumed you would have added the required ``from sklearn.decomposition import PCA``. Sorry for not being more clear

ok now try with my code above again but give as input `X` instead of `self.S_norm.T.shape`. Where X is: ``` X = np.random.normal(size=self.S_norm.T.shape) ```

> Could it be there are nans? No > Is this the correct call? Yes I think this last test proved that the problem is your python installation. The reason...

I don't have other suggestion right now. I can only promise that, in the next weeks, I will test again the notebook and the installation from a couple of different...

The coordinates are arbitrary in tsne and many nonlinear dimensionality reduction outputs and the grid constists of a set of equally spaced points. Given the width and height spanned by...

To add some extra perspective, if a latent variable has the same shape as samples, it is also quite difficult to get to fit the model above in the right...

Thank you for the quick attempt, but no it does not fix the problem. Neither the one without using `gc.collect()` nor the residual leak when garbage collecting.