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userguide:filtres [2010/09/01 16:45] 132.168.73.9 |
userguide:filtres [2011/12/07 18:51] 132.168.72.130 |
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:!: **In a protein group the FIRST protein which matches the rules composition will be set as master.** \\ | :!: **In a protein group the FIRST protein which matches the rules composition will be set as master.** \\ | ||
:!: If no protein in the protein group matches the rules composition, the old one is kept. \\ | :!: If no protein in the protein group matches the rules composition, the old one is kept. \\ | ||
- | :!: If the new master don't have some ambiguous peptide (because they belonging only to the old master) they will be deleted without asking (in contrary of manual master protein changing). | + | :!: If the new master don't match some ambiguous peptides (because they belonging only to the old master) they will be deleted without asking (in contrary of manual master protein changing). |
=== The rules === | === The rules === | ||
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=> You want to set as master only protein belong to HUMAN or MOUSE but never a particular protein which have an accession containing 'P5098'. | => You want to set as master only protein belong to HUMAN or MOUSE but never a particular protein which have an accession containing 'P5098'. | ||
+ | |||
+ | |||
+ | ==== FPR Seeker Filter ==== | ||
+ | |||
+ | The False Positive Rate (FPR) Seeker Filter will search for the best filter to reach the given FPR. | ||
+ | Then launch it with the right parameters.\\ | ||
+ | Nota : 'Best' is defined as the one which can lead to a FPR inferior to the given one while keeping the most forward (if both are equals, ScoreAndRank will be chosen by default)\\ | ||
+ | The FPR is calculated as 2x''Reverse''/(''Reverse''+''Forward''). Where ''Reverse'' is the number of peptide matching on a ''Reverse'' protein and ''Forward'' is the number of peptide matching on a ''Forward'' protein (peptide matching on both type are not counted).\\ | ||
+ | In IRMa you can check the FPR in the [[statistics|statistics window]], into the first tab. | ||
+ | |||
+ | === How to use === | ||
+ | |||
+ | You can access to the FPR Seeker Filter in the Tools menu => Filters => FPR Seeker\\ | ||
+ | {{:userguide:fprseeker-menu.png}}\\ | ||
+ | |||
+ | The following window will be displayed :\\ | ||
+ | {{:userguide:fprseeker-dialog.png}} | ||
+ | |||
+ | === Result === | ||
+ | The result FPR can be seen in statistics window :\\ | ||
+ | {{:userguide:statistics-fpr-closeup.png}}\\ | ||
+ | |||
+ | And the chained filter can be verified in Tools => Filters => Filter History:\\ | ||
+ | {{:userguide:fprseeker-result.png}} | ||
+ | |||
+ |