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dfermin / lucXor

JAVA-based implementation of LuciPHOr that can process any variable PTM.
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About decoy peptides #10

Open ypriverol opened 4 years ago

ypriverol commented 4 years ago

@dfermin:

I'm doing some analysis here and I found that when decoys are not exported some of the peptides in the input are not exported, but when the decoys are exported, then they appear.

isDecoy1 isDecoy2 deltaScore pep1score pep2score globalFLR localFLR
0 0 10.2116 10.2116 0 0.0442 0.0505
0 0 7.5019 7.5019 0 0.0481 0.0723
0 1 5.3761 51.4094 46.0333 0.0659 0.1956

The last peptide will disappear in the first export (default). If I understand correctly is because in the model the second peptide is considered a decoy but what about the first peptide.

dfermin commented 4 years ago

Can you send me the entire output file to look at?