Mode 'full' does not return the correct latent representation

theislab / dca

Deep count autoencoder for denoising scRNA-seq data

Apache License 2.0

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Mode 'full' does not return the correct latent representation #53

Closed valentinwust closed 2 years ago

valentinwust commented 2 years ago

In mode 'full', the original data is overwritten with adata.X = self.model.predict({'count': adata.X, 'size_factors': adata.obs.size_factors}) before the latent representation is created using: adata.obsm['X_dca'] = self.encoder.predict({'count': adata.X, 'size_factors': adata.obs.size_factors}) "X_dca" therefore does not contain the accurate latent representation if this mode is used.

gokceneraslan commented 2 years ago

Thanks! Should be correct now.