Differences

This shows you the differences between two versions of the page.

--- how_to:web:createaggregate [2016/07/05 09:53]
193.48.0.3
+++ how_to:web:createaggregate [2016/07/05 15:54] (current)
193.48.0.3
@@ Line 10: / Line 10: @@
 Note that you can also create an empty dataset to further assemble complex structures using drag and drop in the project tree. However, this way is not favoured.
-{{:how_to:web:dse_new_dataset_based_on_sresults.png?nolink&250 |}}
+{{:how_to:web:dse_new_dataset_based_on_sresults.png?nolink&200 |}}
 \\
 \\
@@ Line 19: / Line 19: @@
 {{ :how_to:web:dse_new_dataset_creation_panel_empty.png?nolink&1000 |}}
-==== Create a simple dataset (single group) ====
+\\
+===== Create a simple dataset (single group) =====
-=== Dataset properties ===
+==== Dataset properties ====
 In the right panel, two text fields allow you to enter a name and description (optional) for your dataset.
@@ Line 40: / Line 42: @@
   * One “Identification” Dataset Node is created for each one of the Result Files you have selected. They take the name of the Result File.
-Once your Identification Dataset has been created, you can see it on the tree, in the left side of the window.
+{{:how_to:web:dse_newly_created_dataset.png?nolink&250 |}}
-The grey icon let you known that it is not yet validated.
-{{:how_to:web:dse_newly_created_dataset.png?nolink&300 |}}
+Once your Identification Dataset has been created, you can see it on the tree, in the left side of the window. You may need to collapse and expand again the //Identifications// node to see it appear.\\
+The white icon let you known that it is not yet validated (becomes green when validated).
-The panel of the Aggregation Node shows a list of your Identification fractions (corresponding to each imported file) and, after the validation process, it will display the Merged Result Summary infos.
+Double click on the aggregation node to open the identification summary. This panel shows a list of your Identification fractions (corresponding to each imported file) and, after the validation process, it will display the Merged Result Summary infos.
+\\
+\\
+\\
+===== Create a complex dataset (automatic grouping) =====
+==== Dataset properties and files selection ====
+Refer to the [[#Create a simple dataset (single group)|previous paragraph]] to know how to do these steps.
+==== Add annotations to files ====
+Once you have selected your result files, click on //Add annotations//. A window shows up, with as many empty lines as selected files.
+{{ :how_to:web:dse_edit_annotations.png?nolink&700 |}}
+=== Example 1: multiple biological groups ===
+Let's say you compare 2 conditions, and you have the following result table (Excel file for instance). The idea is to copy/paste this table to the annotation editor.
+| Result file | Peaklist File | Condition |
+| F078594.dat | OVEMB150205_21.raw.mgf | UPS1 50fmol |
+| F078596.dat | OVEMB150205_23.raw.mgf | UPS1 50fmol |
+| F078592.dat | OVEMB150205_25.raw.mgf | UPS1 50fmol |
+| F078590.dat | OVEMB150205_27.raw.mgf | UPS1 50fmol |
+| F078591.dat | OVEMB150205_12.raw.mgf | UPS1 5fmol |
+| F078595.dat | OVEMB150205_14.raw.mgf | UPS1 5fmol |
+| F078597.dat | OVEMB150205_16.raw.mgf | UPS1 5fmol |
+| F078593.dat | OVEMB150205_18.raw.mgf | UPS1 5fmol |
+  * Select a property to identify the result set with the //Map annotations using...// box. It doesn't need to be the same property as for dataset children name (see [[#Dataset properties|dataset properties]]), so long as it refers to the selected files. In this example, it is convenient to select "Peaklist file name".
+  * In the toolbar at the top of the grid, the annotation //Biological group// is selected by default. Click //Add// to add this column to the grid.
+  * Copy the "Peaklist File" and "Condition" columns of your table, and paste it (using Ctrl + V) in the empty grid of the annotation editor. Note that the files order doesn't matter, so long as there is the right count.
+  * The window should now look like this:
+{{ :how_to:web:dse_edit_annotations_bio_groups.png?nolink&550 |}}
+Click //OK// to register these annotations. The window closes and the files selection has been annotated as shown below (on the left). Click //Create Dataset//. The generated dataset (below, on the right) will have 2 levels of aggregation: biological group (with the copy/pasted names) and top-level (chosen name for dataset).
+{{ :how_to:web:dse_edit_annotations_bio_groups_created.png?nolink&700 |}}
+\\
+\\
+=== Example 2: multiple biological groups and biological samples ===
+Let's take a slightly more complex design, introducing biological replicates for each condition:
+| Result file | Peaklist File | Biological replicate | Condition |
+| F078594.dat | OVEMB150205_21.raw.mgf | BRep 1 | UPS1 50fmol |
+| F078596.dat | OVEMB150205_23.raw.mgf | BRep 1 | UPS1 50fmol |
+| F078592.dat | OVEMB150205_25.raw.mgf | BRep 2 | UPS1 50fmol |
+| F078590.dat | OVEMB150205_27.raw.mgf | BRep 2 | UPS1 50fmol |
+| F078591.dat | OVEMB150205_12.raw.mgf | BRep 1 | UPS1 5fmol |
+| F078595.dat | OVEMB150205_14.raw.mgf | BRep 1 | UPS1 5fmol |
+| F078597.dat | OVEMB150205_16.raw.mgf | BRep 2 | UPS1 5fmol |
+| F078593.dat | OVEMB150205_18.raw.mgf | BRep 2 | UPS1 5fmol |
+**Note**
+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.
+  * As shown previously (see [[#Example 1: multiple biological groups | example 1]]), choose the result set mapping property and add the //Biological group// column.
+  * In the toolbar box, now select the //Biological sample// annotation, and add it by clicking on //Add//.
+  * You can re-arrange the columns order to fit your data table: drag and drop the column headers to move them.
+  * Copy/paste the relevant columns of your table in the annotation editor.
+{{ :how_to:web:dse_edit_annotations_bio_groups_bio_rep.png?nolink&800 |}}
+\\
+{{ :how_to:web:dse_edit_annotations_bio_groups_bio_rep_created.png?nolink&300|}}
+Click //OK// to register the annotations and see them in the creation panel.\\
+Then click //Create Dataset//.\\
+The generated dataset will have 3 levels of aggregation:
+  * top-level (name: chosen in creation panel)
+  * biological groups (names: from annotation editor column)
+  * biological samples (names: from annotation editor column)

Proline

User Tools

Site Tools

Differences

Page Tools