Differences

This shows you the differences between two versions of the page.

--- userguide:filtres [2010/01/12 14:59]
132.168.73.9
+++ userguide:filtres [2011/12/07 18:51]
132.168.72.130
@@ Line 47: / Line 47: @@
 ==== Master Protein Filter ====
 By default the protein groups are represented by a master protein. This master protein is the same as the one defined by mascot.
-If it doesn't suit your needs you have the possibility to change the master proteins one by one in the interface OR, in one step for all the protein group, by using the associated filter.
+If it doesn't suit your needs you have the possibility to change the master proteins one by one in the interface OR, in one step for all the protein groups, by using the associated filter.
-This filter using **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 matches the composition of rules 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 composition of rules, 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 ===
@@ Line 80: / Line 81: @@
 In this example, will be set as master the first protein of each protein group which have :
   * Its Accession number Begins with 'Q70'
-**AND**
+  * **AND**
   * Its Description Contains 'HUMAN'
@@ Line 86: / Line 87: @@
 == Example 2 ==
-{{:userguide:master-filter-window-2.png|}}
+{{:userguide:master-filter-window-2.png|}}\\
 In this example, will be set as master the first protein of each protein group which have :
   * Its Accession number not containing 'P5098'
-**AND**
+  * **AND**
   * Its Description Contains 'HUMAN'
 **OR**
   * Its Accession number not containing 'P5098'
-**AND**
+  * **AND**
   * Its Description Contains 'MOUSE'
 => 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}}

IRMa

User Tools

Site Tools

Differences

Page Tools