prolineconcepts:fdrestimator
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prolineconcepts:fdrestimator [2013/11/21 14:34] 132.168.72.225 [Peptide Spectrum Matches FDR estimation] |
prolineconcepts:fdrestimator [2013/11/27 15:41] (current) 193.48.0.3 |
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| ====== FDR Estimation ====== | ====== FDR Estimation ====== | ||
| - | There are many ways to calculate FDR. Proline implements few of them : | + | There are several ways to calculate FDR depending on the database search type. In Proline the FDR is calculated at peptide and protein levels using the following rules: |
| + | * if the Search has been done on a concatenated Target/Decoy bank, FDR = 2 * nbr DecoyPSM / (nbr TargetPSM + bnr DecoyPSM ). Note: when computing PSM FDR, peptide sequences matching a Target Protein and a Decoy Protein is taken into account in both cases. | ||
| + | * if the Search has been done on a separated Target/Decoy bank, FDR = nbr DecoyPSM / nbr TargetPSM. | ||
| - | ===== Peptide Spectrum Matches FDR estimation ===== | ||
| - | |||
| - | * Default Estimator. The FDR is calculated using following rule | ||
| - | * if Search have been done on a concatenated Target/Decoy bank, FDR = 2 * nbr DecoyPSM / (nbr TargetPSM + bnr DecoyPSM ). PeptideMatches that matches a Target Protein and a Decoy Protein will be count in both case. | ||
| - | * if Search have been done on a separated Target/Decoy bank, FDR = nbr DecoyPSM / nbr TargetPSM. | ||
| - | * **Not actually used** : Competition Based FDR Estimator : Uses FDR described in Navarro et al. (JPR, 2009) | ||
| - | * TO BE DESCRIBED | ||
| - | |||
| - | ===== Protein FDR estimation ===== | ||
| - | |||
| - | FIXME to be described FIXME | ||
prolineconcepts/fdrestimator.1385040876.txt.gz · Last modified: 2013/11/21 14:34 by 132.168.72.225
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