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--- how_to:web:createquantitation [2014/10/01 15:13]
193.48.0.3
+++ how_to:web:createquantitation [2016/07/06 17:13] (current)
193.48.0.3 [Abundance Extraction parameters]
@@ Line 2: / Line 2: @@
 ====== Create a Quantitation ======
-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.
+There are 2 ways to open the Quantitation Creation form:
-Click on the "New Quantitation" button to open the Quantitation Creation Panel.
+  * 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.
+{{:how_to:web:dse_new_lfquant_rclick.png?nolink&300|}}
+{{ :how_to:web:dse_new_lfquant_table.png?nolink&500|}}
+\\
+----
-Note that you can also open it by right-clicking on the Quantitation node or on the Project node itself.
 ===== Title, Type and Method =====
-{{ :how_to:web:dse_quanti_tab_1.png?direct |}}
+{{ :how_to:web:dse_new_lfq_info.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.
+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.
-TODO : details
+Click on //Next// to go to the next step.
-Once you've made your choices, click on "Next".
+----
 ===== Experimental Design =====
-{{ :how_to:web:dse_quanti_tab_2.png?direct |}}
+The //Experimental design// tab is where you define your Groups and Samples.
-The Experimental design tab is where you define your Groups and Samples.
+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.
-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.
+{{ :how_to:web:dse_new_lfq_exp_desing_ddrop.png?nolink&1000 |}}
-In each group, you can manage your sample by using the buttons in the left grid.
-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**
+In the example below, two groups are created this way:
-Once you have prepared all your group and samples, click on the "Next" button.
+{{ :how_to:web:dse_new_lfq_exp_desing_complete.png?nolink&1000 |}}
+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_new_lfq_exp_desing_biorep.png?nolink&1000 |}}
+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 have prepared all your groups and samples, click on the //Next// button.
+----
 ===== Abundance Extraction parameters =====
-{{ :how_to:web:dse_quanti_tab_3.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).
-This tab let you set up you abundance extraction parameters.
+{{ :how_to:web:dse_new_lfq_abundance_extraction.png?nolink&1000 |}}
-TODO : Details
+Tooltips are available to help you understand each parameter.\\
+See [[prolineconcepts:lcmslabelfreequantitationconfig|more details on these parameters]].\\
+See [[prolineconcepts:lcmslabelfreequantitationworkflow|more details on the quantitation process]].
+__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.
+Click on //Next// to go to the last tab.
+----
 ===== Ratios =====
-{{ :how_to:web:dse_quanti_tab_4.png?direct |}}
+The purpose of this tab is to define the ratios between the groups your quantitation will rely on.
+{{ :how_to:web:dse_new_lfquant_ratios.png?nolink&1000 |}}
+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.
-The purpose of this tab is to define the ratios between the groups your quantitation will rely on
+Click the "double arrow" icon to invert numerator and denominator in a ratio.
 ===== Launch the Analysis =====
-When you're done, just press the "Launch Quantitation" button. You will be noticed when the task is finished
+When you're done, just press the //Launch Quantitation// button. You will be noticed when the task is finished

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