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how_to:recomputeretentiontime [2010/07/19 16:46] 132.168.74.230 |
how_to:recomputeretentiontime [2010/08/04 12:10] (current) 132.168.74.230 |
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See [[userguide:retentiontimerecomputing|Retention Time Recomputing principles]] if needed. | 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 ===== | ===== Run the Retention Time Recomputing algorithm ===== | ||
{{ :how_to:rtrecomputingmenu.png |}} | {{ :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 | - 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 | - 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 | - 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. | On top of the dialog, is displayed the User context to process. | ||
**Retention Time Alignment panel** | **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** | **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** | **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** | **Performance panel** | ||
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===== View the Retention Time Recomputing results ===== | ===== 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|}} |