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pFindStudio / pFind3

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Q-values greater than 1 #39

Open mriffle opened 4 years ago

mriffle commented 4 years ago

We have used open pfind version EVA.3.0.11 to conduct a search. When inspecting pFind.spectra we are finding many q-values greater than 1. Most PSMs have a q-value between 0 and 1.8161, which makes no sense. Also, there are many q-values with the exact value of 512, then there are many with the exact value of 1024. The PSMs with a q-value of 1024 also have no peptide ID associated with them, which just compounds the confusion.

Obviously, q-values should not have a value greater than 1. Is this expected behavior? Is this a bug? Are q-values calculated by pFind in a way that we should expect values greater than 1?

cctsou commented 3 years ago

I also have the same question, from the results I got the q values are either 0, 512, or 1024. there is no other value in between. Could you tell us why this happens? perhaps there is some setting we did was not right.

jalew188 commented 3 years ago

512 or 1024 should come from unreliable chemira identifications or other unreliable identifications, just ignore them.