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Nesvilab / FragPipe-Analyst

An easy-to-use and interactive web application for FragPipe
https://fragpipe-analyst-doc.nesvilab.org/
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Error: duplicate 'row.names' are not allowed #20

Closed PostoenkoVI closed 5 months ago

PostoenkoVI commented 6 months ago

Hello Fragpipe team!

I was trying to analyze recent LFQ benchmark dataset with FragPipe (LFQ-MBR workflow, DDA mode) and FragPipe Analyst as a follow up for quantitation using https://fragpipe-analyst.org/. I simply took my combined_proteins.tsv and experiment_annotation.tsv files from FragPipe output and uploaded to the website which followed to "Error: duplicate 'row.names' are not allowed". fragpipe_analyst_out

I'm new to fragpipe, so I was unable to locate an error in my fragpipe analyst input formating. I'm uploading an archive with my combined_proteins.tsv and experiment_annotation.tsv files. Any help would be useful.

Version info: FragPipe version 21.1 MSFragger version 4.0 IonQuant version 1.10.12 Philosopher version 5.1.0 FragPipe_output.zip

Thanks in advance!

hsiaoyi0504 commented 5 months ago

Thanks for the feedback. @PostoenkoVI The key thing and the error message is that you have the same values for the "sample" column in the experiment_annotation.tsv. It should be unique. If multiple samples have only one corresponding quantification column in the quantification report, you should edit the experiment_annotation.tsv to match that. It happens when the files are assigned to the same experiment during performing FragPipe data processing.