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The combined_ion.tsv format exported by FragPipe is used for analysis in DEqMS #47
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Hi, so unfortunately I have no default script for adding peptide counts to the results table. In case you are a little bit familiar with pandas, you could append the counts to the table. It would go something like the code below, you have to adapt the filenames and column names.
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Thanks for your response, and I look forward to your next update! |
Hi, in the newest release, the error with the gene names should now be fixed |
Hi, I just wanted to add a quick comment to this thread. I observe the column annotation error still occurs when using the parquet format. It works as expected when using the tsv report. The parquet report was generated in DIA-NN 1.9.2 |
Thank you for this update! I will look into it. |
I am using the FragPipe software for database searches, and the output file combined_ion.tsv is used for quantification with directLFQ. I plan to perform differential expression analysis using DEqMS, but DEqMS requires peptide counts for each protein to adjust the quantification. How can I use the GUI to add the peptide counts for each protein to the output file, given that this information is not present in the combined_ion.tsv? Additionally, I keep encountering an error 'Could not add additional columns to protein table, printing without additional columns' whenever I try to add gene names.
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