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OSU-BMBL / scDEAL

Deep Transfer Learning of Drug Sensitivity by Integrating Bulk and Single-cell RNA-seq data
Apache License 2.0
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Running Bug #11

Open dada6124357 opened 1 year ago

dada6124357 commented 1 year ago

when I have finished the bulkmodel.py,run the scmodel.py using(python scmodel.py --sc_data "GSE110894" --dimreduce "DAE" --drug "I.BET.762" --bulk_h_dims "256,128" --bottleneck 512 --predictor_h_dims "128,64" --dropout 0.1 --printgene "F" -mod "new" --lr 0.5 --sampling "upsampling" --printgene "F" -mod "new" --checkpoint "False" )following error has occured save/bulk_pre/integrate_data_GSE110894_drug_I.BET.762_bottle_256_edim_512,256_pdim_256,128_model_DAE_dropout_0.1_gene_F_lr_0.5_mod_new_sam_no cannot find correct seperators, return tab as seperator WARNING: It seems you use rank_genes_groups on the raw count data. Please logarithmize your data before calling rank_genes_groups. what is the problem?

juychen commented 1 year ago

Hi, we did not encounter this problem in our enviroment. But someone has a similar experience. Could you please refer to this ?

6

pp.read_sc_file often reports errors because it cannot interpret the separators in the file, even with the pre-built single-cell data. A quick fix I discovered is to force sep=',' in this method.