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--- how_to:web:createquantitation [2014/10/01 15:11]
193.48.0.3 [Launch Quantitation]
+++ how_to:web:createquantitation [2016/07/06 17:13] (current)
193.48.0.3 [Abundance Extraction parameters]
@@ Line 1: / Line 1: @@
-====== Prepare a Quantitation ======
+====== Create a Quantitation ======
-===== Launch Quantitation =====
+There are 2 ways to open the Quantitation Creation form:
+  * Right-click on the //Quantitations// node of the project tree, then click //New Label Free Quantitation// in its menu
+  * Double-click on this node to open the Quantitations table panel. It's empty if you haven't created any quantitation in this project yet. Click the //New Label Free Quantitation// button to open the creation form.
-When you're done, click on the "Launch Quantitation" button. The Task will appear in the tasks panel.
+{{:how_to:web:dse_new_lfquant_rclick.png?nolink&300|}}
-{{ :how_to:web:dse_raw_file_registerer_couples.png?direct&700 |}}
+{{ :how_to:web:dse_new_lfquant_table.png?nolink&500|}}
-If you want to pair files whose names differ, you can proceed as follows :
+\\
-  * Select a file, either Raw or MzDB, in its grid,
-  * Click on the "Put in Couple" button,
-  * Select it in the "Raw & MzDB Couples" grid,
-  * Select the corresponding file of the other format (RAW or MzDB) in its grid,
-  * Click on its "Put in Couple" button.
-After this, you must choose an Instrument Name and select the owner of the file in the users list.
+----
-Finally, click on "Register". Note that this operation will fail if one of your raw file has already been registered.
-Close the Settings Window.
+===== Title, Type and Method =====
-===== Associate RAW Files to Search Results =====
+{{ :how_to:web:dse_new_lfq_info.png?nolink&1000 |}}
-Once you have registered your RAW Files, you must associate them to the Search Results you have imported into your project.
+The first tab of the creation panel, entitled //Information//, let you define a name and an optional description for your quantitation. Type and method are disabled since the label free base on abundance extraction is the only combination available yet.
-{{ :how_to:web:dse_search_result_raw_file_association.png?direct |}}
+Click on //Next// to go to the next step.
-Double-click on the "Search Results" node in your project tree.
+----
-The left grid lists the files you have imported.
-Select one in the grid, then use the right panel's form to search a registered Raw File (by filtering them on its name, its instrument name, its owner and/or its creation date) and select it in the results grid.
-Click on "OK" to associate it with the Result File you have selected in the left panel.
-====== Create a Quantitation ======
+===== Experimental Design =====
-Once you have registered your Raw & MzDB Files and associated Raw Files to you Search Results, you are ready to create a Quantitation.
+The //Experimental design// tab is where you define your Groups and Samples.
-Double-click on the "Quantitations" node of your project tree to show you Quantitations table panel. It's empty if you haven't created any quantitation in this project yet.
+The simplest way to create biological groups (e.g. representing biological conditions) is to drag the validated nodes from the project tree and drop them in the dedicated zone. Drag/drop the nodes one by one.
-Click on the "New Quantitation" button to open the Quantitation Creation Panel.
+{{ :how_to:web:dse_new_lfq_exp_desing_ddrop.png?nolink&1000 |}}
+In the example below, two groups are created this way:
-Note that you can also open it by right-clicking on the Quantitation node or on the Project node itself.
+{{ :how_to:web:dse_new_lfq_exp_desing_complete.png?nolink&1000 |}}
-===== Title, Type and Method =====
+For more complex experimental design, click on //Add New Sample// to add a sample (e.g. biological replicate) to your group. Enter the name of the sample, then drag/drop the corresponding node to the right panel to add it.
-{{ :how_to:web:dse_quanti_tab_1.png?direct |}}
+{{ :how_to:web:dse_new_lfq_exp_desing_biorep.png?nolink&1000 |}}
-The first tab of the Quantitation creation panel let you define a name, a description (optional), choose a type and a method.
-TODO : details
+In most of the cases, the definitions go as following:
+  * biological group = biological condition
+  * biological sample = biological replicate
+  * sample analysis = technical replicate
+However, these definitions are not strict and you can use and adapt the hierarchy to fit your needs. Tooltips are available to help you remind it (place your mouse over the terms to see them).
-Once you've made your choices, click on "Next".
+Once you have prepared all your groups and samples, click on the //Next// button.
+----
-===== Experimental Design =====
+===== Abundance Extraction parameters =====
-{{ :how_to:web:dse_quanti_tab_2.png?direct |}}
+This tab let you set up you abundance extraction parameters. \\
+Depending on your choices, some parameters will become available/unavailable (e.g. clustering parameters are visible only when extracting from MS/MS events).
-The Experimental design tab is where you define your Groups and Samples.
+{{ :how_to:web:dse_new_lfq_abundance_extraction.png?nolink&1000 |}}
-By default, two groups are created and each one contains a sample.
-You can create new groups by clicking on the "Add Group" button in the top bar of the tab.
+Tooltips are available to help you understand each parameter.\\
-In each group, you can manage your sample by using the buttons in the left grid.
+See [[prolineconcepts:lcmslabelfreequantitationconfig|more details on these parameters]].\\
+See [[prolineconcepts:lcmslabelfreequantitationworkflow|more details on the quantitation process]].
-To add a Search Result to one of the samples of the group, select it in the left grid, and **drag and drop a validated result set from your project's tree to the "Sample Analyses" grid**
+__Tip__: If you are creating a quantition that you've already done in the past (i.e. using the same files), select the //Use previous peakel detection// to go much faster. It will skip the long step of peakel detection and use what was previously found instead.
-Once you have prepared all your group and samples, click on the "Next" button.
+Click on //Next// to go to the last tab.
-===== Abundance Extraction parameters =====
+----
-{{ :how_to:web:dse_quanti_tab_3.png?direct |}}
+===== Ratios =====
-This tab let you set up you abundance extraction parameters.
+The purpose of this tab is to define the ratios between the groups your quantitation will rely on.
-TODO : Details
+{{ :how_to:web:dse_new_lfquant_ratios.png?nolink&1000 |}}
-===== Ratios =====
+You can define the ratios:
+  * one by one: specify the numerator and denominator in the //Add single ratio// section
+  * in batch: automatically generate the ratio of each group against a reference group. Use the first section to do it.
+Click the "double arrow" icon to invert numerator and denominator in a ratio.
-{{ :how_to:web:dse_quanti_tab_4.png?direct |}}
+===== Launch the Analysis =====
-The purpose of this tab is to define the ratios between the groups your quantitation will rely on
+When you're done, just press the //Launch Quantitation// button. You will be noticed when the task is finished

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