Differences

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

--- worked_example_prediction_-_train [2015/12/22 12:34] – 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 ======
-**1.** 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]].
 **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:
-  * Expression matrix: {{:brca_genes_vals_bn.txt|}}
+  * Expression matrix: {{::brca_example1_40_exp.txt|}}
-  * Experimental design: {{:brca_normal-basal_ed.txt|}}
+  * Experimental design: {{::brca_example1_40_design.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]].
+**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]].
 **4.** Press the //Prediction// button.
-{{ :hipathia_bar_pred.png?600 |}}
 **5.** In the //Type// panel select //Train new model//.
@@ Line 18: / Line 16: @@
 **6.** In the //Input data panel// select //Expression matrix//. Press the //File browser// of the //Expression matrix file//, and select the desired file.
-{{ :hipathia_work1.png?600 |}}
+**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.
-**7.** 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 |}}
-**8.** Select Human as species (by default).
-**9.** In the //Function level analysis//, check both checkboxes, //Gene ontology// and //Uniprot keywords//.
-**10.** In the //Pathways// panel select all the pathways (by default).
+**8.** Select a machine learning that you want to use.
-**11.** 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".
+**9.** Select Human as species (by default).
-{{ :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".
-**12.** 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.