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--- prolineconcepts:fdrestimator [2013/10/01 11:46]
132.168.72.53
+++ prolineconcepts:fdrestimator [2013/11/27 15:41] (current)
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@@ Line 1: / Line 1: @@
 ====== 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.
-  * Competition Based FDR Estimator : Uses FDR described in Navarro et al. (JPR, 2009)
-    * TO BE DESCRIBED
-===== Protein FDR estimation =====
-FIXME to be described FIXME

Proline