Differences

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--- worked_example_differential_example [2015/12/22 12:32] – mhidalgo
+++ worked_example_differential_example [2017/05/24 14:33] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
-====== Worked example Differential signaling ======
+====== Worked example Differential Module Activity ======
+**1-** Log in into Metabolizer. For further information on this step visit [[logging_in|Logging in]].
-**1-** Log in into HiPathia. For further information on this step visit [[logging_in|Logging in]].
 **2-** We will work with a Breast Cancer dataset from the repository The Cancer Genome Atlas. You can download the expression matrix and the experimental design from these links:
-  * Expression matrix: {{:brca_genes_vals_bn.txt|}}
-  * Experimental design: {{:brca_normal-basal_ed.txt|}}
-**3-** Upload the data to HiPathia in the data panel by clicking on //My data//. For further information on this step visit [[upload_your_data|Upload your data]].
+  * Expression matrix: {{::brca_example1_40_exp.txt|}}
-**4-** Press the //Differential signaling// button.
+  * Experimental design: {{::brca_example1_40_design.txt|}}
+**3-** Upload the data to Metabolizer in the data panel by clicking on //My data//. For further information on this step visit [[upload_your_data|Upload your data]].
-{{ :hipathia_bar_diffsig.png?600 |}}
+**4-** Press the //Activity// button.
-**5-** In the //Input data panel// select //Expression matrix//. Press the //File browser// of the //Expression matrix file//, and select the desired file.
+**5-** Press the //File browser// of the //Expression matrix file//, and select the desired file.
-{{ :hipathia_work1.png?600 |}}
-**6-** In the //Design data// panel select //Two group comparison//. Press the //File browser// of the //Experimental design file//, and select the desired file. Automatically //Condition 1// and //Condition 2// files are selected. Change //Condition 1// to "Tumor" and //Condition 2// to "Normal".
+**6-** Press the //File browser// of the //Experimental design file//, and select the desired file. Automatically //Condition 1// and //Condition 2// files are selected. Change //Condition 1// to "Tumor" and //Condition 2// to "Normal".
-{{ :hipathia_work2.png?600 |}}
+**7-** Select Human as species.
-**7-** Select Human as species (by default).
+**8-** In the //Job information// panel, press the //File browser// button and select the desired output folder. Give a name to the job, for example "BRCA module activity".
-**8-** In the //Function level analysis//, check both checkboxes, //Gene ontology// and //Uniprot keywords//.
-**9-** In the //Pathways// panel select all the pathways (by default).
-**10-** In the //Job information// panel, press the //File browser// button and select the desired output folder. In this case we will use //analysis//. Give a name to the job, for example "BRCA Differential signaling".
-{{ :hipathia_work3.png?600 |}}
 **11-** Press the //Launch job// button. A job will be created and listed in the jobs panel. You can access this panel by clicking on the //My jobs// button.