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veitveit / PhosFake

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peptides removed even if value is set to "0" or "1" (all in or all out) #12

Closed mlocardpaulet closed 3 weeks ago

mlocardpaulet commented 4 weeks ago

When I set PercDetectability to 1, no peptide should be removed at this stage. Here, it seems that one peptide is removed. Something similar happens at the FDR step (in the example pasted below). I suspect that it has to do with WrongIDs. I have not properly checked other steps. 

#MS RUN SIMULATION - Start

 + Noise addition:
  - The MS noise standard deviation is 0 .
  - Noise added to all samples!

 + Detection limits:
  - Keeping  100 % peptides with high detectability score (PeptideRanger).
  - A total of 1 peptides is removed with predicted detectability lower than 0.01485572 .

 + Removing peptide intensities:
  - The percentage of remaining intensities is 100 % and the probabilities of selection depends on intensity values by 0.1 .
  - A total of 1 intensities is removed.

 + Addition of false identification:
  - FDR selected is 0 % and corresponds to 1 peptides.
  - FDR addition finished.

  - PTM re-location finished.

#MS RUN SIMULATION - Finish
veitveit commented 3 weeks ago

Should be solved now