Differences

This shows you the differences between two versions of the page.

--- worked_example_prediction_-_train [2015/12/22 11:36] – mhidalgo
+++ worked_example_prediction_-_train [2017/05/24 14:33] (current) – external edit 127.0.0.1
@@ 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 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 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_example1_40_exp.txt|}}
-  - Press the //Prediction// button.
+  * Experimental design: {{::brca_example1_40_design.txt|}}
-{{ :hipathia_bar_pred.png?600 |}}
+**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]].
-  - In the //Type// panel select //Train new model//.
+**4.** Press the //Prediction// button.
-  - In the //Input data panel// select //Expression matrix//. Press the //File browser// of the //Expression matrix file//, and select the desired file.
+**5.** In the //Type// panel select //Train new model//.
-{{ :hipathia_work1.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.
-  - 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".
+**7.** Press the File browser of the Experimental design file, and select the desired file. All conditions in your design file will be shown on the panel. You do not need to do a selection.
-{{ :hipathia_work2.png?600 |}}
+**8.** Select a machine learning that you want to use.
-  - Select Human as species (by default).
+**9.** Select Human as species (by default).
-  - 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 train model".
-{{ :hipathia_work4.png?600 |}}
+**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 train model".
-  - 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 //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.