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ValueError: Invalid expression matrix in .X. nb mode expects raw UMI counts in .X of the AnnData."

Open wuxiangning opened this issue 5 months ago • 10 comments

hello i have the same issue,when run tnode = sct.train.Trainer(adata)tnode = sct.train.Trainer(adata) its error like this "ValueError Traceback (most recent call last) Cell In[22], line 1 ----> 1 tnode = sct.train.Trainer(adata)

File ~\AppData\Roaming\Python\Python312\site-packages\sctour\train.py:168, in Trainer.init(self, adata, percent, n_latent, n_ode_hidden, n_vae_hidden, batch_norm, ode_method, step_size, alpha_recon_lec, alpha_recon_lode, alpha_kl, loss_mode, nepoch, batch_size, drop_last, lr, wt_decay, eps, random_state, val_frac, use_gpu) 166 X = self.adata.X.data if sparse.issparse(self.adata.X) else self.adata.X 167 if (X.min() < 0) or np.any(~np.equal(np.mod(X, 1), 0)): --> 168 raise ValueError( 169 f"Invalid expression matrix in .X. {self.loss_mode} mode expects raw UMI counts in .X of the AnnData." 170 ) 172 self.n_cells = adata.n_obs 173 self.batch_size = batch_size

ValueError: Invalid expression matrix in .X. nb mode expects raw UMI counts in .X of the AnnData."

but my .X and .raw.X all integers and my seurat counts are also integers,.help!thk!

wuxiangning avatar Sep 21 '24 03:09 wuxiangning