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Noble-Lab / FDRBench

Estimation of false discovery proportion for mass spectrometry proteomics data using entrapment
Apache License 2.0
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Protein FDP calculation example in README not working in windows #2

Open hollenstein opened 2 weeks ago

hollenstein commented 2 weeks ago

Dear developers,

I've run into a minor issue with the example provided in the README for Protein FDP calculation, on a windows computer. java -jar fdrbench-0.0.1.jar -i protein-fdp_protein_input.tsv -level protein -o protein-diann_fdp_protein.csv -score 'score:0' -fold 1 -pick first

Using double quotes for the score column fixed the issue for me. Using single quotes might not work in windows. -score "score:0"

I also have a question regarding the score column. What is the meaning of the ":0"? I glanced over some of the code and I have a feeling it code be related to if a higher score is better? In any case, it would be helpful to document what this does in the parameters section.

Best, David

wenbostar commented 2 weeks ago

Hi David,

Thanks for pointing out this issue. I have improved the documentation for parameter "-score".

Bo