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--- worked_example_prediction [2015/12/22 10:35] – created mhidalgo
+++ worked_example_prediction [2017/05/24 14:33] (current) – external edit 127.0.0.1
@@ 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 Metabolizer. 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 (one of them) 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 matrix1: {{::brca_example1_40_exp.txt|}} (this is the same dataset used for training)
-  - Press the //Differential signaling// button.
+  * Test expression matrix2: {{::brca_2_sample_test.txt|}} (contains 2 new samples, 1 tumor and 1 normal)
-{{ :hipathia_bar_diffsig.png?600 |}}
-  - In the //Input data panel// select //Expression matrix//. Press the //File browser// of the //Expression matrix file//, and select the desired file.
+**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_work1.png?600 |}}
+**4.** Press the //Prediction// button.
-  - 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 model//. 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 |}}
+**6.** In the //Input data panel// select //Expression matrix//. Press the //File browser// of the //Expression matrix file//, and select the desired file, //brca_example1_40_exp.txt//.
-  - Select Human as species (by default).
+**7.** 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 test 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 |}}
+**8.** 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.
-  - 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.