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PyProphet / pyprophet

PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
http://www.openswath.org
BSD 3-Clause "New" or "Revised" License
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Remove m_score filtering? #96

Closed patruong closed 3 years ago

patruong commented 3 years ago

Hi,

Is it possible to remove the m_score filtering. The output seems to be filtered at m_score > 0.05. I have tried increasing the values of ss_initial_fdr and ss_iteration_fdr without success.

Thanks, Patrick

grosenberger commented 3 years ago

You might need to set the correct filter thresholds in pyprophet export, if you used pyprophet ipf, pyprophet peptide or pyprophet protein upstream:

  --max_global_protein_qvalue FLOAT
                                  [format: matrix/legacy] Filter results to
                                  maximum global protein-level q-value.
                                  [default: 0.01]

  --max_global_peptide_qvalue FLOAT
                                  [format: matrix/legacy] Filter results to
                                  maximum global peptide-level q-value.
                                  [default: 0.01]

  --max_rs_peakgroup_qvalue FLOAT
                                  [format: matrix/legacy] Filter results to
                                  maximum run-specific peak group-level
                                  q-value.  [default: 0.05]

  --max_transition_pep FLOAT      [format: legacy] Maximum PEP to retain
                                  scored transitions for quantification
                                  (requires transition-level scoring).
                                  [default: 0.7]