Open mughetto opened 2 years ago
I concur. sciplex3_new.h5ad which is created by processing sciplex_rawchunk{i}.h5ad does not have the value "Vehicle_1.0" in adata.obs.drug_dose_name.values at all, and therefore, there are no cells with adata.obs['control'] = 1. Without the control samples, the training crashes.
What is the solution? use some other drug_dose_name value as the control?
I think should be control_0.0
Hi there,
I've been trying to reproduce the training on sciplex but I get this error with a brand new clone, datasets and conda env:
I have strong suspicion that there is a problem in the preprocessing of sciplex: https://github.com/facebookresearch/CPA/blob/main/preprocessing/sciplex3.ipynb
The cell #6 is probably causing the troubles by making it impossible for adata.obs.control to be anything else than 0. Hence the error above.
Do you have a working version or fix you could share for this please?
Cheers