Differences

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

--- perturbation_effect [2020/01/27 21:15] – krian
+++ perturbation_effect [2021/01/26 16:10] (current) – update old results example ialamo
@@ Line 8: / Line 8: @@
 The **Perturbation effect module** can be accessed from the main menu bar, by clicking on the //Perturbation effect// button.
 {{ :perturbation_effect_form.png?nolink |}}
- ===== INPUT =====
+===== Perturbation effect form =====
+The main page of the tool is a form. This form includes all the information and parameters needed to process a perturbation effect study.
-The main page of the tool is a form. This form includes all the information and parameters needed to process a perturbation effect study. The form is divided in different panels:
+{{ ::perturbationeffectform.png?nolink |}}
+The form is divided in different panels:
 ==== Expression matrix file =====
   * **[[Expression matrix file format |Expression matrix file]]** : Expression matrix provided by ourselves (see how to upload files in [[upload_your_data|Upload your data]]).
+{{ ::expmatrfile.png?nolink |}}
+When we select a gene expression file, the number of samples of this matrix will appear under the “File browser” button as shown below.
+{{ ::pertnumberofsamples.png?nolink |}}
 ==== Sample ====
 Once the file is selected the column names of the expression matrix will be loaded in this panel, we have to select the column to proceed.
-{{ :persurbationeffect.png |}}
+{{ ::samplesperteffectform.png?nolink |}}
 ==== Study information ====
-For further information about this panel, see [[job information|Study information ]]
+This panel includes some parameters in order to identify and save our study.
+  * **Output folder**: If we want to reorganize our studies we can select the folder in which we want save our report. By default the study will be saved in the home in a folder named "Perturbation_effect_study-N", N is an integer number.
+  * **Study name**: We can give a name to our study. This is very useful to later identify it among the other studies listed in the //My studies// list.\\ The default study name is "Perturbation_effect_study-N", N is an integer number.
+  * **Description**: We can give a description to our study.
+{{ ::studyinfopereffectform.png?nolink |}}
+==== Run analysis ====
+Once the form has been filled in, press the //Run analysis// button to launch the study. Your study will be listed in the //My studies// panel.
+{{ ::runanalysis.png?nolink |}}
+Your study will be listed in the //My studies// panel, and a panel called //Browse my studies// will appear showing all your studies and their state. the new study will appear with a **queued** state then **running** state. If everything goes well, the state will be **done** after few minutes(depending on the inputs data and the availability of server).
+All study states are:
+  * **Queued**: The information has been processed and the study has been sent and waits to be processed.
+{{ ::queuedpereff.png?nolink |}}
+  * **Running**: The study is in progress, study can be cancelled using the stop button.
+{{ ::runingperteffect.png?nolink |}}
+  * **Done**: The study has ended and the results are available to visualize and download.
+  * **Cancelled**: The study was canceled before finishing.
+  * **Error**: Sometimes a study can stop returning a error message, you can report and contact us in order to help you to fix it.
+{{ ::studiesperteffect.png?nolink |}}
-Once the form has been filled in, press the //Run analysis// button to launch the study. Your study will be listed in the //My studies// panel.
-===== OUTPUT =====
+===== Perturbation effect report =====
 The results page of the Perturbation effect tool is an ** interactive working environment **. You can **simulate knock outs or over-expressions of one or several genes ** or the ** effect of a drug** in the activity of signaling pathways.
@@ Line 107: / Line 126: @@
 Last update gene list
-==== Interpretation of the results ====
+==== Worked example and Interpretation of the results ====
- For further information about the interpretation of the results, see [[Perturbation effect results|Perturbation effect results]].
+You can find an example of the use of this tool and the interpretation of the results at [[worked_example_perturbation_effect|Worked example: Perturbation effect]].