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--- worked_example_prediction [2015/12/22 10:35]
mhidalgo created
+++ worked_example_prediction [2020/04/03 20:18] (current)
@@ Line 1: / Line 1: @@
 ====== Worked example Prediction - Test ======
-  - 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 test the model with another Breast Cancer dataset from the repository The Cancer Genome Atlas. You can download the expression matrix of the test data from the link:
-    * 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]].
+  * Test expression matrix: {{:brca_genes_vals_bn_test.txt|}}
-  - Press the //Differential signaling// button.
-{{ :hipathia_bar_diffsig.png?600 |}}
+**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 //Input data panel// select //Expression matrix//. Press the //File browser// of the //Expression matrix file//, and select the desired file.
+**4.** Press the //Prediction// button.
-{{ :hipathia_work1.png?600 |}}
+{{ :hipathia_bar_pred.png?600 |}}
-  - 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".
+**5.** In the //Type// panel, select //Test existing predictor//. A window with all the existing models will appear. Select the model you want to use. We will use the model we have created in [[worked_example_prediction_-_train|Worked example Prediction - Train]]. The model information will appear on the right panel.
-{{ :hipathia_work2.png?600 |}}
+{{ :hipathia_work5.png?600 |}}
-  - Select Human as species (by default).
+**6.** In the //Input data panel// select //Expression matrix//. Press the //File browser// of the //Expression matrix file//, and select the desired file, //brca_genes_vals_bn_test.txt//.
-  - 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_work6.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.
+**7.** 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 test model".
+{{ :hipathia_work7.png?600 |}}
+**8.** 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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