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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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EcoTyper failed - EcoTyper_recovery_bulk.R #93

Closed AimSchina closed 2 months ago

AimSchina commented 3 months ago

Hey, thank you for providing this beautiful software! I have been running ecotyper on different public bulk RNA-Seq datasets, and one is giving me trouble:

Running cell state recovery on: B.cells... Running cell state recovery on: PCs... Running cell state recovery on: CD8.T.cells... Running cell state recovery on: CD4.T.cells... Error: No samples were assigned to cell states for cell type: CD4.T.cells Execution halted Running cell state recovery on: NK.cells... Running cell state recovery on: Monocytes.and.Macrophages... Running cell state recovery on: Dendritic.cells... Running cell state recovery on: Mast.cells... Running cell state recovery on: PMNs... Running cell state recovery on: Fibroblasts... Running cell state recovery on: Endothelial.cells... Running cell state recovery on: Epithelial.cells... Error in RunJobQueue() : EcoTyper failed. Please check the error message above! Execution halted

I am wondering whether it fails because samples were not assigned to cell stated for the CD4 T cells, so there cannot be any ecotype assignment...

I would appreciate your feedback, thank you!

cbsteen commented 2 months ago

Yes, without knowing more about the input dataset, I believe you are correct. Perhaps your input dataset is too small for successful recovery.