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--- how_to:recomputeretentiontime [2010/07/19 16:46]
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+++ how_to:recomputeretentiontime [2010/08/04 12:08]
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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, 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.
 **Retention Time Alignment panel**
+  * ''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**
-  * Average:
+  * ''Average'': use average to compute the parent species RT from final child species RTs
-  * Median:
+  * ''Median'': use median to compute the parent species RT from final child species RTs
-  * Weighted average (by score)
+  * ''Weighted average (by score)'': use average weighted by score to compute the parent species RT from final child species RTs
-  * Best score per identification + average:
+  * ''Best score per identification + average'': from final child species, take for each identification the RT of the best score species then use average to compute the parent species RT
-  * Best score per identification + median:
+  * ''Best score per identification + median'': from final child species, take for each identification the RT of the best score species then use median to compute the parent species RT
 **Performance panel**
@@ Line 38: / Line 53: @@
 ===== View the Retention Time Recomputing results =====
+Retention times are replaced by new recomputed values for species belonging strictly to the selected User context.\\
+:!:**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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