Julianus Pfeuffer
Julianus Pfeuffer
Could also be another engine that is just very different from sage such that the combination does not work well. (That's why I would try it alone). Also combinations kind...
Ah I see what you mean now. Percolator fails on the sage-only output before consensusID. Yes that is a problem.
Maybe it is, maybe not. We mostly just pass whatever was in the pin file. I would love to skip all the idxml conversion back and forth but we currently...
Which searchengines were used and where can I see the idXML file? Potentially the consensusXML would work too, for debugging.
That is a bit big. idXML after ConsensusID would be better
I dont know actually where the error starts. Is this not reproducible with a smaller dataset? Like two files of this whole thing?
Hmm I would guess it's the parameters for this dataset. E.g. tolerances, enzymes, modifications. Maybe some are not supported by all engines and then the settings stored in the idxml...
If you are using multiple hits, you probably want some more sophisticated consensus scoring. E.g. PEPMatrix that takes into account the similarities of the top_hits across SEs and allows some...
Could also be used during feature linking but we do not have an algorithm for that yet. So no short-term improvements possible there.
One thing that I am a bit surprised about is that it gets worse. If we are only taking the best PSM per spectrum, nothing should change by adding second-best...