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digitalcytometry / ecotyper

EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
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question in recovery of cell states in scRNA dataset #65

Closed dufeng311 closed 1 year ago

dufeng311 commented 1 year ago

Hi,

I used the following code to recover cell state in a single-cell dataset following the Tutorial 2.1, but an error occurred. Could you please help me check where the error might have occurred?

Rscript EcoTyper_recovery_scRNA.R -d Carcinoma -m example_data/GSE176078/myo.txt -a example_data/GSE176078/meta_data_myo.txt -t 2 -o RecoveryOutput

--> Q&A for bioinformatics, please visit the website: https://www.omicsclass.com/ --> R beginners ? I suggest your learning R language: https://study.omicsclass.com/index The annotation file does not contain column 'Sample'. Will NOT perform ecotype recovery. --> Q&A for bioinformatics, please visit the website: https://www.omicsclass.com/ --> R beginners ? I suggest your learning R language: https://study.omicsclass.com/index

Running cell state recovery on cell type: Monocytes.and.Macrophages... Warning message: More than 2500 cells are available for cell type 'Monocytes.and.Macrophages'. State recovery might take a long time. We recommend using the option -s to downsample the data...

Error in RunJobQueue() : EcoTyper failed. Please check the error message above! Execution halted

BALuca commented 1 year ago

Hi,

Apologize for the issues you are encountering running the code. Unfortunately, it is not obvious from the message where the error might occur. Would it be possible to send us a reproducible example to: ecotyper.stanford@gmail.com?

Best regards, The EcoTyper team

dufeng311 commented 1 year ago

Thank you for the reply