userguide:filtres
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userguide:filtres [2010/01/12 15:08] 132.168.73.247 |
userguide:filtres [2011/12/07 18:51] 132.168.72.130 |
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| This filter use **rules** to determine which protein in the same set must be set as master. To have sufficient complexity you can **composed** multiple rules together.\\ | This filter use **rules** to determine which protein in the same set must be set as master. To have sufficient complexity you can **composed** multiple rules together.\\ | ||
| - | :!: **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 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 === | ||
| Line 97: | Line 98: | ||
| => 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'. | ||
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| + | |||
| + | ==== 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}} | ||
| + | |||
| + | |||
userguide/filtres.txt · Last modified: 2011/12/19 16:32 by 132.168.72.130
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