Differences

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

--- differential_signaling [2015/12/18 16:03] – mhidalgo
+++ differential_signaling [2017/05/24 14:33] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
-====== Differential signaling ======
+===== Module Activity =====
-HiPathia allows us to compute a signal value for each signaling path and each one of our data samples.
+Metabolizer allows us to compute activity value for each module and each one of our data samples.
-Therefore, it allows us to compare the signal value between different conditions.
+Therefore, it allows us to compare the module activity value between different conditions.
-The tools can be accessed from the main menu bar, by clicking on the button //Differential signaling// (see [[workflow|Workflow]]).
+The tool can be accessed from the main menu bar, by clicking on the //Activity// button, see [[workflow|Workflow]] for further information.
-The main page of a the tool is its filling in form. This form includes all the information and parameters that the tool needs to process a job. The form is divided in different panels:
+ === INPUT ===
+The main page of the tool is its filling in form. This form includes all the information and parameters that the tool needs to process a job. The form is divided in different panels:
   * [[Input data|Input data]]
   * [[Design data|Design data]]
   * [[Species|Species]]
-  * [[Parameters|Parameters]]
-  * [[Function level analysis|Function level analysis]]
-  * [[Pathways|Pathways]]
   * [[Job information|Job information]]
+Once the form has been filled in, press the //Launch job// button to launch a job. Your job will be listed in the //My jobs// panel, see [[workflow|Workflow]] for further information.
-==== Input data ====
+=== OUTPUT ===
-In the input data panel, we must introduce the expression data and, optionally, the variant data.
-The **expression data** can be either an:
-  * Expression matrix provided by yourself (see how to upload files in [[upload_your_data|Upload your data]]), or
-  * Expression vector taken from an expression database. In this case, we must choose the tissue database and tissue names.
-The **variant data** must be a VCF file.
+The results page of the module activity tool includes different output results. You can download any table or image showed in the results page by clicking on the name right above it. You can also download calculated module activity values and statistical results by clicking on //**Module values**// and //**Path significance**// respectively. Using module activity values clustering of the samples are represented with heatmap and Principal component analysis (PCA) plots
-==== Design data ====
-The design data panel allows you to choose the kind of experiment you want to perform. You can choose between two main experimental designs:
-  * **Two group comparison**:
-  * **Correlation with continuous variable**:
+The results are divided in different panels:
+  * [[Input Parameters|Input Parameters]]
+  * [[Path values|Module Values]]
+  * [[Pathway viewer|Pathway viewer]]