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--- how_to:recomputeretentiontime [2010/07/20 09:24]
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+++ how_to:recomputeretentiontime [2010/08/04 12:10] (current)
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@@ Line 2: / Line 2: @@
 See [[userguide:retentiontimerecomputing|Retention Time Recomputing principles]] if needed.
+:!: **If you recompute retention time for a given User context, it will not automatically recompute retention time for child contexts (i.e. contexts under the selected context, if exist).\\
+:!: At present, you need to recompute retention time of all your context tree 'manually'. For that, no specific order is needed as final child species are used.**
 ===== Run the Retention Time Recomputing algorithm =====
 {{ :how_to:rtrecomputingmenu.png |}}
+:!: **Required conditions to run the Retention Time Recomputing algorithm:**
+  * **Selected User context must be grouped**
+  * **Protein Grouping on the selected User context must be saved to MSIdb**
+If above conditions are respected, then follow these steps:
   - Select the User context for which you want to recompute retention time
+  - To display the settings dialog:
+      * Right-click on the selected context and select Algorithms→Retention Time→Retention Time Recomputing
+      * Or, from the main toolbar, select MS Identifications→Context→Algorithms→Retention Time→Retention Time Recomputing
   - Go to the ''MS Identifications→Context→Algorithms→Retention Time Recomputing'' to display settings dialog
   - Change algo settings options (see below) if needed and click the ''Ok'' button
-===== Algo settings options =====
+===== Algo settings options (default options are generally optimal) =====
 On top of the dialog, is displayed the User context to process.
@@ Line 17: / Line 30: @@
 **Retention Time Alignment panel**
-  * ''Use alignment coefficients'': if alignment
+  * ''Use alignment coefficients'': if you have previously run the [[how_to:alignretentiontime|Retention Time Alignment algorithm]] (on the same UserContext you want to recompute RT) and if you want to take into account the alignment coefficients in the retention time computing, check this option
 **Outliers panel**
-  * ''Don't take into account outliers'': check this box if you want the algorithm to skip final outliers species (based on Grubbs)
+  * ''Don't take into account outliers'': check this option if you want the algorithm to skip final outliers species (based on [[http://en.wikipedia.org/wiki/Grubbs%27_test_for_outliers|Grubbs method]])
 **Computing Method panel**
@@ Line 41: / Line 54: @@
 Retention times are replaced by new recomputed values for species belonging strictly to the selected User context.\\
-:!:**ATTENTION**: if other contexts exist below, the species retention times are not recomputed.
+:!:**ATTENTION**: if other contexts exist below this selected User context, their species retention times are not recomputed.
 {{:how_to:rtrecomputingresult.png|}}

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