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Teichlab / cellphonedb

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error in Generating user-specific custom database #318

Open Dragonlongzhilin opened 3 years ago

Dragonlongzhilin commented 3 years ago

I want to use custom interaction pairs. But when I use this command, there is a error: command: cellphonedb database generate --user-interactions test.csv --user-interactions-only error: image

The content of text.csv is: image I don't know why?

prete commented 3 years ago

Hi @Dragonlongzhilin could you please check which version of CellPhoneDB and pandas you are using (use pip show CellPhoneDB pandas)? You may be using a pandas version not compatible with CellPhoneDB, that's one outside the required pandas>=1.0.0,<=1.1.4. If that's the case you should pip install -U pandas==1.1.4 to fix it.

Dragonlongzhilin commented 3 years ago

Thank you for your immediate response! I think the version of pandas is ok. image

I solve this problem by converting gene name to uniprot id. But, unfortunately, there is a new error when I run this command: cellphonedb method statistical_analysis --counts-data=gene_name --project-name=Renal --threshold 0.1 --database cellphonedb_user_2021-06-01-21_58.db --output-path=./cellphone_result/RNA/All.user --threads=48 RNA.cell_meta.txt RNA.normailzedCount.txt image

The meta info is: image

prete commented 3 years ago

Meta looks about right, how about your counts file? ValueError: Plan shapes are not aligned sounds similar to #313, but there's no solution there. I wonder if this can be related to python 3.9 or venvs... Is there any chance you could create a Python 3.8 environment and try again?

wangxiv commented 2 years ago

I want to use custom interaction pairs. But when I use this command, there is a error: command: cellphonedb database generate --user-interactions test.csv --user-interactions-only error: image

The content of text.csv is: image I don't know why? you can write interaction_file.csv file like this: id_cp_interaction,partner_a,partner_b,gene_name_a,gene_name_b,ensembl_a,ensembl_b,annotation_strategy CPI-SS111111118,P21854,P06127,CD72,CD5,ENSG00000137101,ENSG00000110448,curated CPI-SS111111116,O43927,P19256,LFA-3,CD2,ENSG00000116815,ENSG00000116824,curated CPI-SS111111115,P22301,Q13651,IL10,IL10RA,ENSG00000136634,ENSG00000110324,curated CPI-SS111111114,P22301,Q08334,IL10,IL10RB,ENSG00000136634,ENSG00000243646,curated CPI-SS111111113,P40933,P31785,IL15,IL2RG,ENSG00000164136,ENSG00000147168,curated CPI-SS111111112,P60568,P01589,IL2,IL2RA,ENSG00000109471,ENSG00000134460,curated CPI-SS999999999,P60568,P14784,IL2,IL2RB,ENSG00000109471,ENSG00000100385,curated