Comments (3)
rmillikin
commented on August 14, 2024
it doesn't remove outlier files; maybe there were no PSMs observed below 1% FDR for those two runs? can you check on that? If this is the case I can report an error message if this happens (but still continue with the analysis, if desired)
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Dmorgen
commented on August 14, 2024
There is definitely data there and the spectrum is quite rich. The only thing, I’m using the MBR function here – no ID’s specifically from these files.
D.
From: Robert Millikin <[email protected]>
Sent: Tuesday, March 31, 2020 8:35 PM
To: smith-chem-wisc/FlashLFQ <[email protected]>
Cc: David Morgenstern <[email protected]>; Author <[email protected]>
Subject: Re: [smith-chem-wisc/FlashLFQ] software threw 2 samples from quant (#89)
it doesn't remove outlier files; maybe there were no PSMs observed below 1% FDR for those two runs? can you check on that? If this is the case I can report an error message if this happens (but still continue with the analysis, if desired)
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rmillikin
commented on August 14, 2024
MBR currently uses identifications in common between two files to create the relative retention time gradient. if a file has no IDs, nothing in the file can be quantified currently. that will probably change at some point, through "blind" feature finding so you can do this kind of thing. it's not currently supported, though
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Related Issues (20)
- Support for Percolator output files HOT 77
- Advice on parameter setting HOT 10
- RT alignment? HOT 2
- Support for more conditions
- FlashLFQ normalization issue HOT 8
- setting up license on linux HOT 2
- FlashLFQ crashed HOT 1
- extra trailing tab in output HOT 1
- will/does it support timsTOF data? HOT 1
- Question about quantification
- crashed - invalid parametrization for the distribution HOT 6
- Enquiry on where the actual namespace for FlashLFQ exists HOT 2
- Question about using with PeptideShaker HOT 3
- No Posterior Error Probability in Bayesian Protein Fold Change Analysis in Command Line tool
- Problem with file name excluding format extension HOT 5
- Shared peptide quantification
- mzML quant error : Index was outside the bounds of the array. HOT 8
- Could not run in Mac OS 13.6
- Header of output file(s) HOT 2
- Remove extra tab from header
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