help!

[chris257-ux]

I run cancercase in my own data , step by step, but meet this error now. why? how to debug? I have been run scPRINT for a lot of days but usually different errors. I just want to use it to create GRN for my scRNA-seq data with annotation.please help me, I really like this method.
TypeError Traceback (most recent call last)
Cell In[29], line 2
1 # create the embedding
----> 2 prostate_adata, metrics = embedder(model, prostate_adata, cache=False, output_expression="none")

TypeError: Embedder.call() got an unexpected keyword argument 'output_expression'

[jkobject]

Hello, I see now that you are right and the notebook is not up to date with the latest version of scPRINT.
I will update it in the coming weeks. In the meantime, can you check out the paper version 1.6.4 ?

[jkobject]

have you tried it?

[jkobject]

I am working on an update for this week

[jkobject]

it is all updated, let me know if it works for you now

[chris257-ux]

Hi,
I run the cancercase.ipynb,
1.when load model load_from_checkpoint ,found the same output "RuntimeError caught: scPrint is not attached to a Trainer." Does it matter?
2.ValueError: Data matrix has wrong shape (47822, 23467), need to be (47822, 3000).
3.my data already processed,so I edit the code, as follow:

prostate_adata.obs.drop(columns="is_primary_data", inplace=True)
preprocessor = Preprocessor(do_postp=False,
    is_symbol=True,
    use_raw=False , 
    force_preprocess=True, 
    min_valid_genes_id=5000
)
prostate_adata = preprocessor(prostate_adata)

and meet Exception and scdataloader ==1.9.2
Exception: Dataset dropped due to too many genes not mapping to it
4.

TypeError Traceback (most recent call last)
Cell In[13], line 2
1 # create the embedding
----> 2 prostate_adata, metrics = embedder(model, prostate_adata, cache=False, output_expression="none")

TypeError: Embedder.call() got an unexpected keyword argument 'output_expression'