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--- worked_example_differential_example [2015/12/22 10:04]
mhidalgo
+++ worked_example_differential_example [2020/04/03 20:18] (current)
@@ Line 1: / Line 1: @@
 ====== Worked example Differential signaling ======
+{{:youtube.png?direct&30|https://www.youtube.com/watch?v=ytyagfQpQPk&feature=youtu.be}}:https://www.youtube.com/watch?v=ytyagfQpQPk&feature=youtu.be
-  - Log in into HiPathia. For further information on this step visit [[logging_in|Logging in]].
-  - 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 ???
+**1-** Log in into HiPathia. For further information on this step visit [[logging_in|Logging in]].
-  - 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]].
-  - Press the //Differential signaling// button.
+**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:
-  - In the //Input data panel// select //Expression matrix//. Press the //File browser// of the //Expression matrix file//, and select the desired file.
-  - 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".
+  * Expression matrix: {{:brca_genes_vals_bn.txt|}}
-  - Select Human as species (by default).
+  * Experimental design: {{:brca_normal-basal_ed.txt|}}
-  - In the //Function level analysis//, check both checkboxes, //Gene ontology// and //Uniprot keywords//.
-  - In the //Pathways// panel select all the pathways (by default).
+**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]].
-  - 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".
-  - 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.
+**4-** Press the //Differential signaling// button.
+{{ :hipathia_bar_diffsig_5.png?600 |}}
+**5-** In the //Input data panel//. 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".
+{{ :hipathia_work2.png?600 |}}
+**7-** Select Human as species (by default).
+**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 //Study information// panel, press the //File browser// button and select the desired output folder. In this case we will use //analysis_BRCA//. Give a name to the study, for example "BRCA Differential signaling".
+{{ :hipathia_work3_5.png?600 |}}
+**11-** Press the //Run analysis// button. A study will be created and listed in the studies panel. You can access this panel by clicking on the //My studies// button.

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