theislab / scib

Benchmarking analysis of data integration tools
MIT License
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Questions about runDESC in the integration part #298

Open HelloWorldLTY opened 2 years ago

HelloWorldLTY commented 2 years ago

Hi, I found that for my dataset, if I use runDESC via scIB, I will receive such error: image However, I can successfully run my method based on the tutorial of DESC https://eleozzr.github.io/desc/tutorial.html The code is: adata_desc = desc.train(adata, dims=[adata.shape[1], 32, 16], tol=0.005, n_neighbors=10, batch_size=256, louvain_resolution=[0.8], save_dir="result_pbmc3k", do_tsne=True, learning_rate=300, do_umap=True, num_Cores_tsne=4, save_encoder_weights=True)

I wonder why. Thanks.

LuckyMD commented 2 years ago

Are you running both scripts in the same environment? We had some difficulties getting a consistent environment set up for DESC and scGen, which have clashing dependencies. It might be worth checking if the dependencies are not consistent in your scib environment.