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CostaLab / CrossTalkeR

R package to do the Ligand Receptor Analysis Visualization
https://costalab.github.io/CrossTalkeR/
MIT License
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No CellPhoneDB interacions found in this input. #45

Open ankurnaqib opened 2 years ago

ankurnaqib commented 2 years ago

Hi. I was running the following command: cellphonedb method statistical_analysis cellphonedb_meta.txt cellphonedb_countv2.txt --threads 30 --counts-data hgnc_symbol and I was getting the "No CellPhoneDB interacions found in this input." error. My data has around 82k cells divided into 6 sample groups, so I followed the suggestions on page https://github.com/Teichlab/cellphonedb/issues/309 and modified my command to :

cellphonedb method statistical_analysis cellphonedb_meta.txt cellphonedb_countv2.txt --threads 30 --counts-data hgnc_symbol --subsampling --subsampling-log False --subsampling-n um-cells 50 --iterations=10 but I am getting the same error. My data has HGNC gene symbols. Any help would be appreciated. Thank you.

jsnagai commented 2 years ago

Hi @ankurnaqib

82k cells divided into 6 sample groups...Do you mean 6 different phenotypes or 6 cell populations?

Best

gabumon0 commented 1 year ago

Is there because of the species? not human, so the gene intersect is zero?

seoyounglee6445 commented 1 year ago

i solved this problem. Because my dataset was not normalized dataset. recommended check your dataset.