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Teichlab / cellphonedb

MIT License
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Gene format missmatch. #365

Open dfc-1931475 opened 2 years ago

dfc-1931475 commented 2 years ago

hello, i came acoss a problem, when i use the cellphonedb method statistical_analysis command, the software always return "[WARNING] Gene format missmatch. Using gene type 'ensembl' expects gene names to start with 'ENSG' but some genes seem to be in another format. Try using '--counts-data hgnc_symbol' if all counts are filtered". i have checked my counts data many times, it still does not work.
More importantly， i tried the example data you supplied， the same bug occured again，i don think its the data format fault, could you please check this soonly? i need graduate for this what can i do to deal with this issue? m_hfd_meta.txt image

LASTLY, IT seems that i have found the right answer about the second error from the ISSUE #344 However, i still confused by the problem, why it does not work when i used the ENSG name(stable id).

prete commented 2 years ago

Hi @dfc-1931475 it's hard to tell without the full command you used to launch this. The error is probably on your counts data rather than the your meta data. You'll need to double check that the first column of your counts file to see if it is actually in the right format.