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--- worked_example_prediction_-_train [2015/12/22 10:42]
mhidalgo created
+++ worked_example_prediction_-_train [2020/04/03 20:18] (current)
@@ Line 1: / Line 1: @@
 ====== Worked example Prediction - Train ======
-  - Log in into HiPathia. 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]].
-  - 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|}}
+**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:
-    * Experimental design: {{:brca_normal-basal_ed.txt|}}
-  - 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_genes_vals_bn.txt|}}
-  - Press the //Prediction// button.
+  * 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]].
+**4.** Press the //Prediction// button.
 {{ :hipathia_bar_pred.png?600 |}}
-  - In the //Type// panel select //Train new model//.
+**5.** In the //Type// panel select //Train new predictor//.
+**6.** In the //Input data panel// select //Expression matrix//. Press the //File browser// of the //Expression matrix file//, and select the desired file.
+{{ :hipathia_Pred_work1.png?600 |}}
+**7.** In the //Design data// panel select //Class predictor//. 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".
-  - In the //Input data panel// select //Expression matrix//. Press the //File browser// of the //Expression matrix file//, and select the desired file.
+{{ :hipathia_Pred_work2.png?600 |}}
-{{ :hipathia_work1.png?600 |}}
+**8.** Select Human as species (by default).
-  - 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 |}}
+**9.** In the //Pathways// panel select all the pathways (by default).
-  - Select Human as species (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_BRCA//. Give a name to the job, for example "BRCA train model".
-  - In the //Function level analysis//, check both checkboxes, //Gene ontology// and //Uniprot keywords//.
-  - In the //Pathways// panel select all the pathways (by default).
-  - 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 |}}
+{{ :hipathia_work4.png?600 |}}
-  - 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.
+**11.** Press the //Run analysis// button. A job will be created and listed in the jobs panel. You can access this panel by clicking on the //My jobs// button.

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