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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 recovery "undefined columns" issue #2

Closed othmanalsawaf closed 3 years ago

othmanalsawaf commented 3 years ago

Hi,

Thank you for developing this great tool!

I have some issues running ecotyper recovery with a small set of 100 bulk RNA seq samples. I have previously successfully run your bulk lymphoma and lung examples without any issues.

I have a tab de-limited file as per the tutorial instructions (TPM_count_matrix_ecotyper_short.txt) with a TPM expression matrix and a table with annotations, also tab-delimited (annotations_short.txt).

I use the bash command: Rscript EcoTyper_recovery_bulk.R -d 'Carcinoma' -m "TPM_count_matrix_ecotyper_short.txt" -a "annotations_short.txt" -c disease_status -o output_4

But I get the following error:

Running cell state recovery on: PMNs... Running cell state recovery on: NK.cells... Running cell state recovery on: PCs... Running cell state recovery on: Dendritic.cells... Running cell state recovery on: Fibroblasts... Running cell state recovery on: B.cells... Running cell state recovery on: Mast.cells... Running cell state recovery on: CD4.T.cells... Running cell state recovery on: CD8.T.cells... Running cell state recovery on: Monocytes.and.Macrophages... Running cell state recovery on: Epithelial.cells... Running cell state recovery on: Endothelial.cells... Running ecotype recovery... Error in [.data.frame(top_annotation, , x) : undefined columns selected Calls: heatmap_simple ... unlist -> lapply -> FUN -> unique -> [ -> [.data.frame Execution halted Error in RunJobQueue() : EcoTyper failed. Please check the error message above!`

When I run the script without the annotation file, it seems to work fine, but when I include the annotation terms, I always get the same error. Do you have an idea what the issue might be?

Thanks ever so much!

Best wishes Othman

annotations_short.txt TPM_count_matrix_ecotyper_short.txt

BALuca commented 3 years ago

Dear Othman,

Thank you for flagging out the issue, and providing the data for debug. We could isolate the problem and fix it. The latest commit to the repository includes these fixes.

Please let us know if you encounter any other issues.

Best regards, The EcoTyper team

othmanalsawaf commented 3 years ago

Wow, thank you for your swift reply and solving the issue so quickly! Works perfectly now. Will close this issue, thanks a million.

Best wishes Othman